Contacts of the helix formed by residues 75 - 97 (chain A) in PDB entry 2CTF
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 PRO 75 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER 4.9 8.1 - - - +
26A PHE* 4.8 1.7 - - + -
58A LYS* 4.1 47.8 - - + +
59A VAL* 4.9 0.2 - - + -
74A GLY* 1.3 81.9 - - - +
76A THR* 1.3 55.8 + - + +
77A GLU* 2.5 25.3 + - + +
78A ASP* 2.7 34.0 + - + +
79A VAL* 2.7 14.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 5.8 6.1 - - + +
23A ALA 5.9 3.1 - - - +
25A SER 5.1 2.1 + - - +
27A THR* 3.7 32.2 + - - +
74A GLY 3.5 3.8 + - - -
75A PRO* 1.3 70.5 - - + +
77A GLU* 1.3 66.2 + - + +
79A VAL* 4.2 5.4 - - - -
80A SER* 3.1 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 2.5 13.9 + - + +
76A THR* 1.3 84.8 - - + +
78A ASP* 1.3 64.5 + - + +
80A SER* 3.6 3.5 + - - -
81A VAL* 3.5 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN 4.7 0.9 - - - +
56A MET* 2.9 40.5 - - - +
57A PRO* 5.3 0.3 - - - +
58A LYS* 4.8 5.4 - - - +
59A VAL* 2.7 31.7 - - + +
75A PRO* 2.7 24.6 + - + +
77A GLU* 1.3 74.4 - - + +
79A VAL* 1.3 57.7 + - - +
80A SER 3.0 2.0 - - - -
81A VAL* 2.7 29.0 + - - +
82A ALA* 2.8 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.7 11.7 - - + +
29A SER* 4.5 13.5 - - - +
59A VAL* 4.0 9.2 - - + -
72A LEU* 3.9 22.8 - - + +
73A GLU 4.0 2.7 - - - -
74A GLY* 2.9 54.5 - - - +
75A PRO* 2.7 16.5 + - + +
76A THR* 4.1 5.4 - - - +
78A ASP* 1.3 72.9 - - - +
80A SER* 1.3 56.4 + - - +
82A ALA* 3.9 2.2 - - - +
83A GLN* 2.9 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 3.1 22.5 + - - -
77A GLU 3.6 5.6 - - - -
78A ASP 3.0 0.4 - - - -
79A VAL* 1.3 76.0 - - - +
81A VAL* 1.3 62.4 + - - +
83A GLN* 3.3 14.5 + - - +
84A GLU* 3.0 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A MET* 3.8 19.7 - - + -
77A GLU* 3.5 16.6 - - + +
78A ASP* 2.7 16.4 + - - +
80A SER* 1.3 71.3 - - - +
82A ALA* 1.3 59.3 + - - +
84A GLU* 3.5 8.0 + - - +
85A GLN* 3.0 37.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
52A ILE* 4.7 10.9 - - + +
56A MET* 4.1 14.8 - - + +
59A VAL* 3.6 31.9 - - + -
61A ILE* 5.6 0.7 - - + -
72A LEU* 4.9 3.6 - - + -
78A ASP* 2.8 18.4 + - - +
79A VAL 4.0 1.6 - - - +
81A VAL* 1.3 74.2 - - - +
83A GLN* 1.3 66.7 + - - +
84A GLU 3.0 1.3 - - - -
85A GLN* 3.0 16.0 + - - +
86A ILE* 3.1 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.1 23.5 + - - -
30A SER 5.0 2.0 + - - -
31A VAL* 3.5 28.7 - - + +
72A LEU* 4.4 10.4 - - + +
79A VAL* 2.9 28.6 + - + +
80A SER* 3.3 19.0 + - - +
82A ALA* 1.3 76.5 - - - +
84A GLU* 1.3 66.2 + - + +
86A ILE* 3.5 11.1 + - - +
87A GLU* 3.2 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.0 21.3 + - - +
81A VAL* 3.6 7.5 - - - +
82A ALA 3.0 0.4 - - - -
83A GLN* 1.3 80.0 - - + +
85A GLN* 1.3 67.4 + - + +
86A ILE 3.0 1.6 - - - -
87A GLU* 3.0 25.2 + - + +
88A GLY* 3.2 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.1 21.4 - - + +
55A GLN* 5.7 1.8 - - - +
56A MET* 3.3 28.0 - - + +
81A VAL* 3.0 27.2 + - + +
82A ALA* 3.0 7.7 + - - +
84A GLU* 1.3 77.3 - - + +
86A ILE* 1.3 60.8 + - + +
88A GLY* 3.7 2.1 + - - -
89A MET* 3.5 24.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
31A VAL* 4.8 7.2 - - + -
41A ILE* 4.3 5.8 - - + -
52A ILE* 4.7 10.8 - - + -
61A ILE* 4.6 15.7 - - + -
63A PHE* 5.8 0.2 - - + -
70A ILE* 3.6 37.2 - - + -
72A LEU* 4.2 26.0 - - + -
82A ALA 3.2 16.6 - - - +
83A GLN* 3.7 10.1 - - - +
84A GLU 3.0 0.6 - - - -
85A GLN* 1.3 76.2 - - - +
87A GLU* 1.3 56.9 + - - +
88A GLY 3.0 5.2 - - - -
89A MET* 3.1 18.7 - - + +
90A VAL* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.6 25.5 - - + +
32A ALA 5.5 0.7 + - - -
83A GLN* 3.2 29.4 + - - +
84A GLU* 3.0 17.2 + - + +
86A ILE* 1.3 77.2 - - - +
88A GLY* 1.3 60.1 + - - +
90A VAL* 4.2 5.8 - - - +
91A LYS* 3.6 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU 3.2 10.4 + - - -
85A GLN 3.7 3.1 + - - -
86A ILE 3.0 0.8 - - - -
87A GLU* 1.3 77.3 - - - +
89A MET* 1.3 64.8 + - - +
90A VAL 3.3 0.2 - - - -
91A LYS* 3.3 5.9 + - - +
92A ASP* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 3.3 48.2 - - + +
48A ASN* 4.6 15.0 - - + +
49A LEU* 6.3 1.6 - - + -
52A ILE* 4.2 21.3 - - + -
63A PHE* 5.8 0.4 - - + -
85A GLN 3.5 17.9 + - - +
86A ILE* 3.1 28.3 - - + +
88A GLY* 1.3 72.6 - - - +
90A VAL* 1.3 64.8 + - + +
92A ASP* 3.3 6.4 + - - +
93A LEU* 3.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 5.8 1.6 - - + -
32A ALA 4.7 5.2 - - - +
33A ALA* 4.1 13.5 - - + -
34A PRO* 3.8 26.2 - - + -
37A LEU* 4.9 2.4 - - + +
41A ILE* 3.6 30.3 - - + -
86A ILE* 2.9 29.2 + - + +
87A GLU* 4.5 5.8 - - - +
89A MET* 1.3 77.3 - - + +
91A LYS* 1.3 62.3 + - - +
93A LEU* 3.7 8.6 + - - +
94A ILE* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU 3.6 17.1 + - - +
88A GLY* 3.3 6.4 + - - +
89A MET 3.2 0.6 - - - -
90A VAL* 1.3 79.3 - - - +
92A ASP* 1.3 61.1 + - - +
94A ILE* 3.2 8.9 + - + +
95A ASN* 2.8 62.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
88A GLY 3.2 10.2 + - - +
89A MET* 3.3 10.1 + - - +
91A LYS* 1.3 78.1 - - - +
93A LEU* 1.3 63.6 + - + +
95A ASN* 3.4 10.7 + - - +
96A ARG* 3.0 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 4.9 4.1 - - + -
37A LEU* 4.4 22.9 - - + -
40A PHE* 4.1 29.6 - - + +
41A ILE* 4.4 27.1 - - + +
89A MET* 3.0 30.7 + - + +
90A VAL* 3.8 10.8 - - - +
92A ASP* 1.3 78.9 - - + +
94A ILE* 1.3 62.0 + - - +
96A ARG* 3.4 7.4 + - - +
97A SER* 3.3 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 4.6 9.4 - - + -
36A TRP* 3.9 27.8 - - + -
37A LEU* 4.5 2.9 - - + -
90A VAL* 3.2 32.3 + - + +
91A LYS* 3.2 10.2 + - + +
93A LEU* 1.3 75.0 - - - +
95A ASN* 1.3 65.2 + - - +
97A SER* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 2.8 55.5 + - - +
92A ASP* 3.6 9.5 - - - +
94A ILE* 1.3 80.0 - - - +
96A ARG* 1.3 64.4 + - + +
97A SER 3.9 4.0 - - - +
98A GLY 4.2 7.8 - - - +
99A PRO* 4.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 3.0 31.1 + - - +
93A LEU* 3.5 11.2 - - - +
95A ASN* 1.3 79.4 - - + +
97A SER* 1.3 60.7 + - - +
98A GLY 3.2 3.1 + - - -
99A PRO* 3.9 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TRP* 4.7 20.3 - - - -
93A LEU 3.3 8.1 + - - -
94A ILE* 2.8 25.6 + - - +
96A ARG* 1.3 76.2 - - - +
98A GLY* 1.3 65.8 + - - +
----------------------------------------------------------
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