Contacts of the helix formed by residues 81 - 101 (chain A) in PDB entry 3T79
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 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP 5.1 1.0 - - - +
80A ILE* 1.3 80.8 - - - +
82A ASN* 1.3 55.7 + - - +
83A ASN* 2.8 22.4 - - - +
84A ASP* 3.1 14.5 + - + +
85A VAL* 2.8 34.5 + - - +
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Residues in contact with ASN 82 (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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76A ARG* 3.1 28.1 + - - -
80A ILE 3.5 2.7 + - - -
81A GLU* 1.3 67.7 - - - +
83A ASN* 1.3 70.1 + - - +
85A VAL* 2.8 22.8 - - - +
86A LEU* 3.0 18.0 + - - +
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Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 2.8 28.3 - - - +
82A ASN* 1.3 75.3 - - - +
84A ASP* 1.3 75.6 + - - -
86A LEU* 2.7 48.3 + - + +
87A VAL* 2.8 14.6 + - + +
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.2 21.8 - - - +
81A GLU* 3.1 21.9 + - + +
83A ASN* 1.3 92.1 + - - +
85A VAL* 1.3 66.1 + - - +
87A VAL* 2.9 32.5 + - - +
88A LEU* 2.9 13.3 + - - +
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.6 31.8 - - + +
75A SER* 3.4 25.8 - - - +
76A ARG* 3.9 31.6 - - + +
80A ILE* 3.9 8.7 - - + +
81A GLU 2.8 20.0 + - - +
82A ASN* 2.8 31.6 - - - +
84A ASP* 1.3 72.2 - - - +
86A LEU* 1.3 57.2 + - - +
88A LEU* 3.0 12.6 - - + +
89A GLN* 2.9 24.1 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 5.9 1.3 - - - +
82A ASN* 3.0 24.8 + - - +
83A ASN* 2.7 34.1 + - + +
85A VAL* 1.3 72.2 - - + +
87A VAL* 1.3 66.1 + - + +
89A GLN* 3.1 13.1 + - - +
90A GLN* 2.1 58.3 + - + +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.9 17.4 + - - +
83A ASN* 2.8 26.2 + - + +
84A ASP* 2.9 22.4 + - - +
86A LEU* 1.3 77.8 - - + +
88A LEU* 1.3 70.3 + - + +
90A GLN* 3.2 10.7 - - - +
91A ARG* 3.0 22.3 + - - +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.6 3.1 - - + +
46A SER* 5.0 3.8 - - - +
47A GLN* 4.1 33.7 - - + +
50A ILE* 4.1 22.4 - - + -
71A MET* 6.1 1.6 - - + -
72A ILE* 5.5 5.8 - - + -
75A SER* 5.8 9.4 - - - +
84A ASP* 2.9 7.5 + - - +
85A VAL* 3.0 17.0 - - + +
87A VAL* 1.3 84.1 - - + +
89A GLN* 1.3 63.1 + - - +
91A ARG* 2.8 15.3 + - + -
92A LEU* 2.9 49.4 + - + +
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Residues in contact with GLN 89 (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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72A ILE* 3.7 36.1 - - + +
85A VAL* 2.9 12.8 + - - +
86A LEU* 3.3 17.5 - - - +
88A LEU* 1.3 75.0 - - - +
90A GLN* 1.3 71.2 + - - +
92A LEU* 3.1 5.8 + - - +
93A TYR* 2.9 66.1 + - + -
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Residues in contact with GLN 90 (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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86A LEU* 2.1 53.7 + - + +
87A VAL* 3.2 14.6 - - - +
88A LEU 3.1 0.2 - - - -
89A GLN* 1.3 88.6 + - - +
91A ARG* 1.3 64.7 + - - +
93A TYR* 3.3 8.8 + - - +
94A GLY* 2.9 20.1 + - - -
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Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLN* 3.5 49.7 + - + +
48A LYS* 5.8 1.2 - - - +
51A VAL* 3.4 37.3 - - + +
87A VAL 3.0 11.1 + - - +
88A LEU* 2.8 14.8 + - + +
90A GLN* 1.3 73.0 - - - +
92A LEU* 1.3 57.4 + - + +
94A GLY* 3.2 3.2 + - - +
95A LEU* 2.9 26.9 + - - +
279A PRO* 2.9 33.7 - - + +
281A PHE* 4.9 9.1 - - - -
303A PRO* 4.0 20.6 - - - +
306A TYR* 2.5 30.9 + - - +
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Residues in contact with LEU 92 (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 GLN* 6.1 0.7 - - - -
50A ILE* 4.5 18.2 - - + -
51A VAL* 4.7 12.1 - - + -
54A ILE* 4.8 0.2 - - + -
68A CYS* 3.8 48.1 - - + +
71A MET* 4.5 11.2 - - + -
72A ILE* 4.2 10.5 - - + -
88A LEU* 2.9 40.3 + - + -
89A GLN* 3.1 8.5 + - - +
91A ARG* 1.3 74.4 - - + +
93A TYR* 1.3 70.0 + - + +
95A LEU* 3.2 20.0 + - + +
96A VAL* 3.0 26.7 + - - +
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.1 24.8 - - + +
68A CYS* 4.9 4.7 - - + -
69A ASP* 4.0 13.4 + - - -
72A ILE* 4.2 11.1 - - + +
89A GLN* 2.9 58.7 + - + +
90A GLN* 3.8 8.7 - - - +
92A LEU* 1.3 75.5 - - + +
94A GLY* 1.3 64.1 + - - +
96A VAL* 2.8 33.4 - - + +
97A LYS* 2.9 8.2 + - - +
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Residues in contact with GLY 94 (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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90A GLN 2.9 15.3 + - - -
91A ARG* 3.2 4.9 + - - -
93A TYR* 1.3 74.1 - - - +
95A LEU* 1.3 60.9 + - - +
97A LYS* 3.1 8.9 + - - +
98A LEU* 2.9 24.1 + - - +
276A PRO* 5.4 2.3 - - - +
277A GLN* 5.5 8.3 + - - +
306A TYR* 4.6 4.7 - - - -
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 4.6 16.8 - - + +
54A ILE* 3.9 39.9 - - + -
55A ALA* 5.2 1.6 - - + -
68A CYS* 5.3 2.2 - - - -
91A ARG 2.9 15.7 + - - +
92A LEU* 3.2 22.6 + - + +
94A GLY* 1.3 72.0 - - - +
96A VAL* 1.3 64.9 + - + +
98A LEU* 3.2 8.5 - - + +
99A LEU* 2.9 34.7 + - + +
305A PHE* 3.6 33.7 - - + -
306A TYR* 3.7 18.4 + - + +
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Residues in contact with VAL 96 (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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64A PRO* 4.0 28.9 - - + -
65A LEU* 4.8 17.9 - - + -
68A CYS* 4.3 11.7 - - - -
92A LEU 3.0 19.1 + - - +
93A TYR* 2.8 25.6 - - + +
95A LEU* 1.3 74.4 - - + +
97A LYS* 1.3 76.4 + - + +
99A LEU* 2.5 32.7 + - - +
100A GLU* 2.9 23.7 + - + +
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Residues in contact with LYS 97 (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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93A TYR 2.9 8.8 + - - +
94A GLY* 3.1 10.7 + - - +
96A VAL* 1.3 85.5 - - + +
98A LEU* 1.3 52.1 + - - +
100A GLU* 5.2 2.0 - - - -
101A PHE* 2.6 47.2 + - + +
273A GLN 3.3 21.4 + - - -
274A GLU* 3.1 28.5 + - + +
275A TRP 4.0 2.0 - - - +
276A PRO* 3.8 21.5 - - + -
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Residues in contact with LEU 98 (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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94A GLY 2.9 9.4 + - - +
95A LEU 3.2 10.1 - - - +
96A VAL 2.7 2.4 + - - -
97A LYS* 1.3 77.6 - - - +
99A LEU* 1.3 67.9 + - + +
101A PHE* 3.3 2.4 + - - +
276A PRO* 3.3 28.4 - - + +
277A GLN 4.4 3.8 - - - +
305A PHE* 4.8 6.3 - - + -
306A TYR* 3.2 61.2 - - + +
309A LYS* 3.1 38.8 - - + +
310A MET* 3.4 27.1 - - + -
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Residues in contact with LEU 99 (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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54A ILE* 4.2 18.8 - - + -
55A ALA* 5.0 9.0 - - + -
61A ALA* 4.2 28.5 - - + +
64A PRO* 4.2 8.5 - - + -
95A LEU* 2.9 39.9 + - + +
96A VAL* 2.5 11.2 + - - +
98A LEU* 1.3 78.9 - - + +
100A GLU* 1.3 65.8 + - + +
101A PHE 4.0 2.4 - - - +
305A PHE* 4.2 20.0 - - + -
309A LYS* 4.2 8.0 + - - +
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Residues in contact with GLU 100 (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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61A ALA 5.6 1.3 - - - +
62A LYS 4.3 16.5 - - - +
63A ASP* 5.7 0.2 - - - -
64A PRO* 4.7 13.8 - - + +
65A LEU* 6.0 3.5 - - - +
96A VAL* 2.9 26.1 + - + +
97A LYS* 5.1 1.3 - - - -
99A LEU* 1.3 78.0 - - + +
101A PHE* 1.3 68.9 + - - +
102A ASP* 3.0 6.1 + - - +
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Residues in contact with PHE 101 (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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97A LYS* 2.6 31.6 + - + +
98A LEU* 3.3 5.1 + - - +
99A LEU 4.0 0.2 - - - +
100A GLU* 1.3 74.0 - - - +
102A ASP* 1.3 79.6 + - - +
103A TYR* 3.4 24.5 - + - -
106A VAL* 4.0 10.3 - - + -
274A GLU* 3.4 29.2 - - - -
275A TRP* 3.2 43.1 - + - -
276A PRO* 3.2 24.2 - - + -
309A LYS* 2.6 36.7 + - - -
388D GLU* 4.8 5.2 - - - -
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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
------------------------------------------------------------
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