Contacts of the helix formed by residues 76 - 99 (chain A) in PDB entry 3RR1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY* 1.3 73.1 - - - -
77A PRO* 1.3 76.9 - - - +
78A ILE 3.3 2.6 + - - -
79A LEU 3.6 0.2 + - - -
80A MET* 3.0 26.4 + - - +
238A PHE* 4.0 13.5 - - - -
405A CL 3.1 11.1 - - - +
76B GLY* 4.4 2.0 - - - -
77B PRO* 3.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLY* 1.3 83.1 - - - +
78A ILE* 1.3 59.0 + - - +
81A SER* 2.7 28.6 + - - -
238A PHE* 3.7 21.9 - - + -
261A HIS* 2.8 23.8 + - + +
72B PHE* 3.8 16.2 - - + -
73B TYR* 4.0 5.2 - - + -
74B ARG 3.6 14.6 - - - +
75B GLY 3.4 29.2 - - - +
76B GLY* 4.1 0.7 - - - +
79B LEU* 4.1 10.1 - - + -
405B CL 3.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 4.0 12.8 - - + -
40A THR* 3.8 36.3 - - + +
41A VAL* 4.1 12.6 - - + +
44A ALA* 3.9 20.9 - - + -
76A GLY 3.3 0.4 - - - -
77A PRO* 1.3 74.9 - - - +
79A LEU* 1.3 65.8 + - - +
81A SER* 3.3 5.2 + - - -
82A ALA* 3.1 20.6 + - - +
405A CL 3.5 8.2 - - + +
40B THR* 4.1 7.6 - - + -
72B PHE* 3.6 28.7 - - + -
78B ILE* 4.4 4.7 - - + -
79B LEU* 3.9 15.5 - - + -
405B CL 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 4.3 19.5 - - + -
48A LEU* 4.4 13.1 - - + +
67A MET 6.2 0.4 - - - +
72A PHE* 3.6 35.4 - - + -
73A TYR 4.1 3.8 - - - +
75A GLY* 3.7 28.7 - - - +
78A ILE* 1.3 78.7 - - - +
80A MET* 1.3 58.0 + - - +
82A ALA* 3.3 4.4 + - - +
83A ILE* 2.9 39.7 + - + +
405A CL 3.2 12.9 - - + +
37B ARG* 4.0 25.6 - - - +
77B PRO* 4.5 1.1 - - + -
78B ILE* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 4.0 27.4 - - + -
68A TYR* 3.8 31.9 - - + -
75A GLY* 3.6 20.0 - - - +
76A GLY 3.0 22.9 + - - +
79A LEU* 1.3 73.6 - - - +
81A SER* 1.3 59.6 + - - +
83A ILE* 4.2 9.9 - - + -
84A ALA* 2.8 25.5 + - - +
238A PHE* 3.4 34.3 - - + +
239A SER* 4.2 8.5 - - - -
261A HIS* 3.1 24.4 - - + +
262A ALA 4.6 0.7 - - - +
263A GLY* 3.6 13.1 + - - -
267A GLU* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 3.4 11.4 - - - +
33A VAL* 3.7 23.2 + - - +
41A VAL* 4.5 7.4 - - - +
77A PRO 2.7 24.2 + - - -
78A ILE 3.3 4.6 + - - -
79A LEU 3.3 0.4 - - - -
80A MET* 1.3 75.9 - - - +
82A ALA* 1.3 64.5 + - - +
84A ALA* 3.2 2.8 + - - +
85A GLY 3.1 18.5 + - - -
260A SER 3.6 13.9 + - - -
261A HIS* 2.9 23.1 + - - -
72B PHE* 5.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 4.7 0.4 - - - -
41A VAL* 4.3 4.4 - - + +
44A ALA* 3.8 16.4 - - + -
45A VAL* 3.7 40.8 - - + +
48A LEU* 3.8 13.5 - - + -
78A ILE 3.1 8.1 + - - +
79A LEU 3.3 6.9 + - - +
81A SER* 1.3 74.8 - - - +
83A ILE* 1.3 63.6 + - - +
85A GLY* 3.3 2.8 + - - -
86A ILE* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.7 18.8 - - + -
64A TRP* 3.3 38.4 - - + +
67A MET* 3.8 22.8 - - + +
68A TYR* 3.7 37.5 - - + +
75A GLY* 6.1 0.2 - - - -
79A LEU* 2.9 25.5 + - + +
80A MET* 3.8 19.3 - - + +
82A ALA* 1.3 74.1 - - - +
84A ALA* 1.3 59.6 + - - +
86A ILE* 3.2 2.1 + - - +
87A ASP* 2.9 28.2 + - - +
263A GLY* 4.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A MET 2.8 22.5 + - - +
81A SER 3.2 1.8 + - - +
83A ILE* 1.3 75.0 - - - +
85A GLY* 1.3 61.4 + - - +
87A ASP* 3.7 1.4 - - - +
88A GLN* 3.1 30.6 + - - +
259A LEU 3.3 23.1 - - - +
260A SER* 3.5 21.3 - - - -
263A GLY 3.7 2.5 - - - +
264A GLY* 3.3 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.7 18.6 - - - +
30A GLY* 3.3 13.0 - - - -
31A GLU 4.0 7.6 - - - -
32A PRO* 4.0 18.1 - - - +
81A SER 3.1 13.2 + - - -
82A ALA 3.3 3.3 + - - -
84A ALA* 1.3 73.8 - - - +
86A ILE* 1.3 65.6 + - - +
88A GLN* 4.4 0.7 - - - -
89A ALA 3.3 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.1 16.2 - - + -
18A LEU* 4.1 13.2 - - + -
20A VAL* 5.3 2.7 - - + -
45A VAL* 4.1 13.5 - - + +
48A LEU* 3.7 22.7 - - + -
52A LEU* 3.6 27.4 - - + -
67A MET* 3.6 34.5 - - + -
82A ALA 3.1 17.9 + - - +
83A ILE 3.9 3.1 - - - +
85A GLY* 1.3 75.6 - - - +
87A ASP* 1.3 64.4 + - - +
89A ALA* 3.1 5.9 + - - +
90A LEU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.4 12.1 - - - +
64A TRP* 3.4 12.0 - - + +
67A MET* 4.9 2.2 - - + +
83A ILE 2.9 17.1 + - - +
84A ALA 3.7 4.5 - - - +
86A ILE* 1.3 78.2 - - - +
88A GLN* 1.3 61.0 + - - +
90A LEU* 3.3 9.9 + - - +
91A TRP* 3.0 30.2 + - - -
263A GLY 3.9 12.8 - - - +
264A GLY* 4.2 0.4 - - - -
265A ILE 2.8 27.0 + - - -
266A THR* 2.6 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP 3.7 4.3 - - - +
30A GLY* 3.9 4.9 - - - -
31A GLU* 2.7 37.4 + - - +
84A ALA 3.1 17.7 + - - +
85A GLY 3.7 3.6 - - - +
86A ILE 3.3 0.2 - - - -
87A ASP* 1.3 76.9 + - - +
89A ALA* 1.3 58.6 + - - +
91A TRP* 3.3 6.4 + - - +
92A ASP* 2.9 27.2 + - - +
259A LEU 3.1 27.9 + - - +
260A SER* 3.1 20.8 + - - +
264A GLY* 4.8 5.8 - - - -
265A ILE* 4.7 5.8 - - + -
291A ILE* 3.6 9.3 - - - +
292A ALA* 4.4 2.1 + - - +
295A ALA* 3.9 26.1 - - + +
348A LEU* 3.7 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 10.1 - - + -
20A VAL* 3.5 27.8 - - + -
28A GLY* 3.5 7.0 - - - +
29A TRP 3.3 28.4 + - - +
85A GLY 3.3 1.8 + - - -
86A ILE 3.1 9.2 + - - +
88A GLN* 1.3 80.0 - - - +
90A LEU* 1.3 57.6 + - - +
92A ASP* 3.2 3.7 + - - +
93A ILE* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.0 15.3 - - + -
20A VAL* 4.6 6.3 - - + -
52A LEU* 4.7 1.1 - - + -
57A PRO* 3.9 28.8 - - + +
60A ILE* 3.6 35.8 - - + +
63A LEU* 3.8 33.0 - - + -
64A TRP 5.5 0.2 - - - +
67A MET* 4.9 3.1 - - + -
86A ILE* 2.9 37.3 + - + +
87A ASP* 3.3 9.6 + - - +
89A ALA* 1.3 72.5 - - - +
91A TRP* 1.3 60.6 + - - +
93A ILE* 3.2 14.1 + - + +
94A LYS* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.6 20.6 - - + +
61A ASN* 6.0 3.4 - - - -
87A ASP* 3.0 38.2 + - - -
88A GLN 3.6 6.7 - - - +
90A LEU* 1.3 72.9 - - - +
92A ASP* 1.3 66.1 + - - +
94A LYS* 3.3 15.1 + - + +
95A GLY 3.0 19.6 + - - -
102A VAL* 3.5 29.4 - - + +
105A LEU* 3.8 36.1 - - + -
106A LEU* 3.7 29.8 - - + -
265A ILE* 3.6 33.7 - - + +
266A THR* 3.0 26.6 + - + +
348A LEU* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY* 3.4 1.4 - - - -
29A TRP* 2.9 34.1 + - - +
88A GLN 2.9 13.8 + - - +
89A ALA 3.2 9.2 + - - +
91A TRP* 1.3 77.2 - - - +
93A ILE* 1.3 61.6 + - - +
96A LYS* 3.1 57.4 + - - +
346A PRO 4.2 0.3 - - - +
347A GLY* 3.4 3.1 - - - -
348A LEU* 2.9 43.2 + - + +
349A GLY 4.4 1.2 + - - -
350A VAL* 5.0 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 5.5 1.1 - - + -
20A VAL* 3.7 33.0 - - + +
22A THR* 3.9 14.8 - - + -
26A VAL* 4.1 15.9 - - + +
27A THR 4.0 3.8 - - - -
28A GLY* 3.5 22.4 - - - +
57A PRO* 4.0 26.2 - - + -
58A SER* 6.4 0.2 - - - -
89A ALA 2.9 20.0 + - - +
90A LEU* 3.5 15.9 - - + +
91A TRP 3.2 0.2 - - - -
92A ASP* 1.3 74.7 - - - +
94A LYS* 1.3 55.9 + - - +
96A LYS* 3.1 4.5 + - - +
97A VAL* 2.8 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 5.6 0.7 - - - +
58A SER* 2.9 45.1 + - - +
60A ILE* 3.7 19.1 - - + -
90A LEU 3.0 15.6 + - - +
91A TRP* 3.8 28.9 - - + +
93A ILE* 1.3 77.1 - - - +
95A GLY* 1.3 58.1 + - - +
97A VAL* 3.4 5.1 + - - +
98A LEU* 2.9 48.6 + - + +
105A LEU* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP 3.0 12.0 + - - -
94A LYS* 1.3 77.1 - - - +
96A LYS* 1.3 55.8 + - - +
98A LEU 3.4 0.2 + - - -
99A GLY* 2.8 24.3 + - - -
100A VAL* 2.9 32.2 + - - -
102A VAL* 4.8 0.7 - - - -
105A LEU* 3.9 13.8 - - - +
346A PRO* 3.6 0.3 - - - +
347A GLY* 3.6 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.7 19.0 - - + +
27A THR* 2.7 31.5 + - - +
29A TRP* 4.5 8.3 - - - -
92A ASP* 3.1 36.0 + - - +
93A ILE 3.1 7.9 + - - +
95A GLY* 1.3 73.7 - - - +
97A VAL* 1.3 64.6 + - - +
99A GLY* 3.3 10.9 + - - -
346A PRO* 3.8 28.0 - - + +
350A VAL 4.8 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 5.1 20.6 - - + -
26A VAL* 4.2 20.0 - - + -
93A ILE* 2.8 37.4 + - + +
94A LYS* 3.7 7.4 - - + +
96A LYS* 1.3 74.2 - - - +
98A LEU* 1.3 73.7 + - + +
99A GLY 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LYS* 2.9 36.0 + - + +
97A VAL* 1.3 88.1 - - + +
99A GLY* 1.3 61.9 + - - +
100A VAL* 3.4 12.0 + - + +
105A LEU* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 2.8 8.9 + - - -
96A LYS 3.3 7.5 + - - -
97A VAL 3.3 5.1 + - - -
98A LEU* 1.3 77.7 - - - +
100A VAL* 1.3 62.4 + - - +
101A PRO* 4.9 0.3 - - - +
346A PRO* 3.8 21.1 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il