Contacts of the helix formed by residues 64 - 82 (chain A) in PDB entry 3PMM
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 GLU 64 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 5.8 2.0 - - - +
55A ILE* 3.4 29.1 - - - +
56A ASP 4.4 0.2 - - - +
57A THR* 3.6 39.8 - - - +
63A TRP* 1.3 84.8 + - - +
65A TRP* 1.3 75.0 + - + +
66A THR* 3.0 18.8 - - + +
67A HIS* 2.9 24.2 + - + +
68A GLY 3.4 7.1 + - - -
108A ASN* 4.2 7.3 + - - +
109A THR* 5.1 4.5 - - - -
112A PRO* 4.3 6.4 - - - +
156A LEU* 5.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU* 1.3 83.0 - - + +
66A THR* 1.3 76.6 + - + +
68A GLY* 3.0 3.3 + - - -
69A VAL* 3.0 31.2 + - + +
108A ASN* 3.4 59.5 + - + +
111A ALA* 4.0 4.8 - - - +
171A MSE 3.7 27.8 - - + -
230A ARG* 5.2 3.4 - - - -
234A TRP* 3.6 33.7 - + - -
362A TYR* 3.4 50.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR 4.4 2.0 + - - +
64A GLU* 3.4 14.9 - - + +
65A TRP* 1.3 114.8 - - + +
67A HIS* 1.3 56.6 + - - +
69A VAL* 3.4 3.6 + - - +
70A GLY* 3.0 24.9 + - - -
361A PRO* 4.0 11.4 - - + -
362A TYR* 3.9 21.3 - - + -
365A ALA* 4.5 4.0 - - - +
380A IMD 2.6 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR 4.4 1.6 - - - -
59A GLY 2.9 24.4 + - - -
60A TRP* 3.5 30.8 + + + -
62A GLY* 3.2 29.0 + - - -
63A TRP 3.5 2.0 - - - -
64A GLU* 2.9 35.7 + - + +
66A THR* 1.3 73.4 + - - +
68A GLY* 1.3 61.0 + - - +
70A GLY 4.5 0.2 - - - +
71A LEU* 2.8 38.0 + - + +
93A TRP* 3.7 25.4 - - + +
112A PRO* 4.9 0.2 - - + -
380A IMD 3.4 31.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.4 4.8 + - - -
65A TRP 3.0 8.6 + - - -
67A HIS* 1.3 80.1 - - - +
69A VAL* 1.3 61.0 + - - +
71A LEU* 3.9 2.5 - - - +
72A TYR* 3.1 18.2 + - - +
111A ALA* 3.9 4.3 - - - +
112A PRO* 3.7 33.9 - - - +
115A THR* 4.4 1.9 + - - -
388A FMT 3.2 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 3.0 27.9 + - + +
66A THR* 4.0 5.2 - - - +
67A HIS 3.3 0.4 - - - -
68A GLY* 1.3 76.0 - - - +
70A GLY* 1.3 63.9 + - - +
72A TYR* 3.3 4.9 + - - +
73A GLY* 3.1 17.3 + - - -
170A MSE 5.1 3.1 - - + -
171A MSE 3.8 32.8 - - + -
234A TRP* 4.4 8.7 - - + -
237A MSE 5.1 1.8 - - + -
362A TYR* 5.8 1.3 - - + -
365A ALA* 3.9 15.3 - - + +
366A MSE 4.4 14.1 - - + -
369A LEU* 3.7 24.6 - - + +
388A FMT 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.9 15.9 - - - +
60A TRP* 5.0 1.3 - - - -
66A THR 3.0 13.8 + - - -
67A HIS* 3.8 2.7 - - - -
69A VAL* 1.3 74.9 - - - +
71A LEU* 1.3 64.2 + - - +
73A GLY* 3.2 2.1 + - - -
74A ILE* 3.0 33.7 + - - +
365A ALA* 3.6 20.5 - - - +
368A ILE* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.9 28.2 - - + -
67A HIS 2.8 32.5 + - - +
68A GLY* 3.9 3.6 - - - +
70A GLY* 1.3 71.7 - - - +
72A TYR* 1.3 58.0 + - - +
74A ILE* 3.4 5.5 + - + +
75A TYR* 2.8 31.7 + - - +
90A ILE* 4.0 32.1 - - + +
93A TRP* 3.5 43.7 - - + -
94A PHE* 4.1 11.9 - - + -
112A PRO* 4.1 7.6 - - + -
115A THR* 3.5 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.1 18.4 + - - +
69A VAL 3.5 4.5 - - - +
70A GLY 3.2 0.2 - - - -
71A LEU* 1.3 78.3 - - - +
73A GLY* 1.3 57.8 + - - +
75A TYR* 3.3 8.0 + + - +
76A GLN* 2.9 61.6 + - + +
114A LEU* 3.5 30.3 - - + +
115A THR* 3.2 14.6 - - - +
118A TYR* 4.3 17.8 + + - -
170A MSE 3.6 28.9 - - + -
174A LEU* 4.3 1.8 - - + +
241A ASP* 2.6 36.9 + - - +
300A TYR* 4.3 2.2 - + - -
369A LEU* 4.1 11.0 - - + -
382A FMT 4.2 12.9 + - - -
388A FMT 4.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL 3.1 10.8 + - - -
70A GLY 3.2 3.1 + - - -
72A TYR* 1.3 74.7 - - - +
74A ILE* 1.3 63.9 + - - +
76A GLN* 3.2 3.6 + - - +
77A TYR* 3.1 19.2 + - - +
365A ALA 5.0 0.4 - - - -
368A ILE* 3.6 22.1 - - - +
369A LEU* 3.5 28.2 - - - +
372A THR* 4.3 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 4.0 28.0 - - + +
35A LEU* 4.3 7.0 - - + -
36A VAL* 4.5 0.7 - - + -
60A TRP* 4.2 17.3 - - + -
70A GLY 3.0 18.8 + - - +
71A LEU* 3.8 6.1 - - + +
73A GLY* 1.3 74.4 - - - +
75A TYR* 1.3 64.0 + - - +
77A TYR* 3.3 3.6 + - - +
78A TYR* 2.9 21.0 + - - +
86A MSE 3.6 49.5 - - + +
89A ILE* 4.0 20.9 - - + -
90A ILE* 3.8 10.8 - - + -
368A ILE* 3.9 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 2.8 21.6 + - - +
72A TYR* 3.6 12.6 - + - +
73A GLY 3.2 0.4 - - - -
74A ILE* 1.3 74.9 - - - +
76A GLN* 1.3 58.8 + - + +
78A TYR* 3.2 17.1 + + - +
79A GLN* 2.7 75.6 + - + +
90A ILE* 3.5 13.6 - - + +
115A THR* 3.9 13.2 - - + -
118A TYR* 3.4 45.1 + + + +
119A ARG* 4.2 13.0 - - - -
122A GLU* 3.2 32.7 + - - +
382A FMT 4.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 2.9 52.7 + - + +
73A GLY* 3.2 5.6 + - - +
75A TYR* 1.3 77.7 - - + +
77A TYR* 1.3 57.2 - - - +
79A GLN* 3.6 10.9 - - - +
80A GLN* 3.0 30.3 + - - +
300A TYR* 2.8 36.9 + - - -
304A LYS* 5.1 2.4 + - - -
307A ARG* 5.7 1.0 + - - -
369A LEU* 3.5 14.3 - - + +
372A THR* 3.8 15.9 - - + +
373A GLU* 4.6 8.0 + - - +
376A ARG* 5.5 0.7 + - - -
382A FMT 3.8 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 3.4 33.1 + - + +
28A ILE* 3.8 22.0 - - + -
29A ARG* 4.4 9.8 - - + +
73A GLY 3.1 9.5 + - - +
74A ILE 3.6 7.2 - - - +
76A GLN* 1.3 77.6 - - - +
78A TYR* 1.3 60.6 + - - +
80A GLN* 3.3 1.8 + - - +
81A THR* 2.8 54.4 + - + +
83A ASP* 3.9 19.2 + - + -
86A MSE 3.8 33.0 - - + -
372A THR* 3.6 29.3 - - + +
375A LEU* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 2.9 13.7 + - - +
75A TYR* 3.5 24.7 - + - +
77A TYR* 1.3 79.3 - - - +
79A GLN* 1.3 62.6 + - - +
81A THR* 4.0 4.7 - - - -
82A GLY* 2.7 47.7 + - - -
83A ASP 3.4 20.9 - - - +
84A ILE* 4.7 4.4 - - + +
86A MSE 4.3 1.8 - - + -
87A ARG* 3.5 51.6 + - + +
90A ILE* 5.0 0.9 - - + -
119A ARG* 3.8 10.9 + - - -
122A GLU* 3.2 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 2.7 54.7 + - + +
76A GLN* 3.6 9.8 - - - +
77A TYR 3.3 0.2 - - - -
78A TYR* 1.3 80.7 - - - +
80A GLN* 1.3 61.3 + - - +
82A GLY 4.5 1.2 + - - -
118A TYR* 4.3 5.1 - - - -
376A ARG* 4.5 14.6 + - - +
382A FMT 3.2 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 5.5 1.0 + - - -
76A GLN 3.0 16.4 + - - +
77A TYR* 3.7 4.3 - - - +
79A GLN* 1.3 79.9 - - - +
81A THR* 1.3 66.6 + - + +
372A THR* 3.0 37.3 + - - +
375A LEU* 3.3 26.7 - - - +
376A ARG* 3.7 34.7 - - - +
379A PHE* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 4.5 13.2 - - - +
77A TYR* 2.8 47.7 + - + +
80A GLN* 1.3 93.0 - - + +
82A GLY* 1.3 61.0 + - - +
83A ASP* 3.1 26.7 + - - +
379A PHE* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 2.7 32.3 + - - -
79A GLN 4.5 1.0 + - - -
80A GLN 3.8 0.6 - - - -
81A THR* 1.3 72.5 - - - +
83A ASP* 1.3 63.4 + - - +
84A ILE* 3.0 19.8 + - - +
----------------------------------------------------------
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