Contacts of the helix formed by residues 67 - 79 (chain A) in PDB entry 3M5B
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 SER 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.9 1.1 - - - -
65A GLY 4.1 1.8 + - - -
66A ILE* 1.3 75.5 - - - +
68A PRO* 1.4 75.3 - - - +
69A SER* 3.7 9.0 + - - -
70A THR* 3.0 32.1 + - - -
71A PHE* 3.0 22.3 + - - +
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Residues in contact with PRO 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.6 35.4 - - + +
36A GLY* 5.6 0.7 - - - -
37A SER 5.7 0.4 - - - +
38A GLN* 3.6 41.7 - - + +
40A PHE* 3.6 10.9 - - + -
66A ILE 4.5 0.2 - - - +
67A SER* 1.4 86.1 - - - +
69A SER* 1.3 61.8 + - - +
71A PHE* 4.5 0.7 - - + +
72A ALA* 3.0 26.0 + - - +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 5.5 0.2 - - - +
67A SER* 3.2 8.8 + - - -
68A PRO* 1.3 80.5 - - - +
70A THR* 1.3 61.8 + - - +
72A ALA* 3.5 5.9 + - - +
73A GLN* 3.3 28.6 + - - +
89A GLU* 4.2 14.6 + - - -
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Residues in contact with THR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 4.4 3.1 - - + -
67A SER* 3.0 27.0 + - - -
69A SER* 1.3 78.3 - - - +
71A PHE* 1.3 62.8 + - - +
73A GLN* 3.3 14.7 + - - +
74A LEU* 3.2 18.0 + - - +
89A GLU 5.4 0.7 + - - -
92A PRO* 3.7 28.8 - - - +
93A LEU* 3.7 18.4 - - + +
96A ALA* 3.7 28.9 - - + -
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.6 35.2 - - + -
35A VAL* 4.1 14.8 - - + -
40A PHE* 3.7 42.0 - + + -
47A LEU* 6.1 0.7 - - + -
54A LEU* 5.5 5.4 - - + -
62A LEU* 3.5 24.5 - - + -
66A ILE* 4.3 9.6 - - + +
67A SER 3.0 15.9 + - - +
68A PRO* 4.0 4.0 - - + +
70A THR* 1.3 78.7 - - - +
72A ALA* 1.3 56.3 + - - +
74A LEU* 3.3 20.0 + - + +
75A LEU* 2.9 47.0 + - + +
96A ALA* 6.0 0.2 - - - -
100A LEU* 4.0 18.8 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.7 21.5 - - + -
68A PRO 3.0 18.6 + - - +
69A SER* 3.8 7.4 - - - +
71A PHE* 1.3 76.3 - - - +
73A GLN* 1.3 58.6 + - + +
75A LEU* 3.4 4.5 + - - +
76A ASN* 3.0 39.1 + - - +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER* 3.3 18.0 + - - +
70A THR* 3.3 19.3 + - - +
71A PHE 3.3 0.2 - - - -
72A ALA* 1.3 75.8 - - + +
74A LEU* 1.3 64.0 + - - +
76A ASN* 3.5 6.2 + - - +
77A PHE* 3.0 19.4 + - - +
83A VAL* 3.4 31.6 - - + +
84A GLU 4.7 5.0 + - - +
85A LEU* 3.3 26.2 - - - +
89A GLU* 3.0 34.4 + - - +
93A LEU* 4.0 16.2 - - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 6.2 0.4 - - + -
54A LEU* 4.6 9.2 - - + -
70A THR 3.2 12.3 + - - +
71A PHE* 3.6 29.8 - - + +
73A GLN* 1.3 75.8 - - - +
75A LEU* 1.3 67.1 + - + +
77A PHE* 3.2 4.9 + - - +
78A VAL* 3.1 40.9 + - + +
93A LEU* 3.9 6.2 - - + +
96A ALA* 4.1 12.8 - - + +
97A ALA* 4.0 31.6 - - - +
100A LEU* 4.1 15.5 - - + -
102A VAL* 4.3 15.3 - - + -
105A LEU* 4.0 22.2 - - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.8 22.7 - - - +
33A ILE* 5.7 0.4 - - + -
40A PHE* 4.0 28.0 - - + -
41A PRO 4.0 17.7 - - - +
42A ALA* 4.4 6.5 - - + -
47A LEU* 4.1 23.6 - - + -
71A PHE* 2.9 34.3 + - + +
72A ALA* 3.9 5.2 - - - +
74A LEU* 1.3 78.9 - - + +
76A ASN* 1.3 66.1 + - - +
78A VAL* 3.3 7.0 + - + +
79A TYR* 3.2 47.5 + - + -
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Residues in contact with ASN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 2.8 38.3 - - - +
72A ALA* 3.0 27.5 + - - +
73A GLN* 3.8 7.2 - - - +
75A LEU* 1.3 75.1 - - - +
77A PHE* 1.3 63.1 + - - +
79A TYR* 3.1 9.7 + - - +
80A GLY 3.2 0.3 + - - -
81A GLU* 3.1 48.7 + - + +
82A SER 5.4 0.7 - - - +
83A VAL* 4.7 6.5 - - + -
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.1 13.7 - - + -
9A PRO 3.4 28.0 - - - -
10A SER* 2.7 34.8 + - - -
11A PRO* 3.7 18.8 - - + -
12A TYR* 3.7 8.4 - + - -
73A GLN 3.0 15.0 + - - +
74A LEU 3.2 10.1 + - - +
76A ASN* 1.3 74.8 - - - +
78A VAL* 1.3 63.2 + - + +
80A GLY 3.1 8.1 + - - -
81A GLU 3.5 11.6 + - - -
83A VAL* 4.1 12.0 - - + +
102A VAL* 5.0 0.9 - - + -
104A SER* 3.8 27.4 - - - -
105A LEU* 3.8 46.9 - - + -
108A ALA* 4.6 5.2 - - + -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.9 18.1 - - - +
18A VAL* 3.9 11.3 - - - +
46A VAL* 4.1 21.7 - - + +
47A LEU* 4.3 20.4 - - + -
50A VAL* 4.0 25.6 - - + +
54A LEU* 5.7 1.8 - - + -
74A LEU* 3.1 30.7 + - + +
75A LEU* 3.3 11.0 + - + +
77A PHE* 1.3 78.1 - - + +
79A TYR* 1.3 61.7 + - + +
80A GLY 3.3 0.9 + - - -
102A VAL* 4.3 22.7 - - + -
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Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.6 16.8 - - + +
19A GLN* 5.3 0.7 + - - -
21A ALA* 3.9 16.2 - - + -
22A ALA* 3.6 41.2 - - + +
25A ARG* 3.7 39.5 - - - +
42A ALA* 3.5 8.4 - - + -
43A HIS* 2.8 53.6 + + - +
46A VAL* 4.1 19.1 - - + -
47A LEU* 5.6 1.1 - - + -
75A LEU* 3.2 46.3 + - + +
76A ASN 3.1 6.0 + - - +
78A VAL* 1.3 76.3 - - + +
80A GLY* 1.3 58.3 + - - +
81A GLU* 3.5 6.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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