Contacts of the helix formed by residues 76 - 95 (chain A) in PDB entry 2P82
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).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.8 1.7 - - - -
72A ASP* 2.8 35.9 + - - +
75A TRP* 1.3 87.1 - - - +
77A CYS* 1.3 62.4 + - - +
78A MET 3.4 1.6 - - - -
79A LEU* 3.1 14.9 + - - +
80A ARG* 3.0 22.8 + - - +
128A ILE* 4.7 0.2 - - - -
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Residues in contact with CYS 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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57A TYR* 3.6 16.8 - - + +
75A TRP 3.4 1.6 + - - -
76A GLY* 1.3 75.8 - - - +
78A MET* 1.3 55.8 + - - +
80A ARG* 3.3 5.8 + - - +
81A CYS* 3.0 31.4 + - - -
145A TRP* 3.2 30.1 - - - -
262A ASN* 3.3 19.5 - - - -
264A ALA* 3.4 11.0 - - + -
280A PRO* 3.8 11.6 - - + +
281A HIS* 3.3 37.0 - - + +
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Residues in contact with MET 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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75A TRP 4.9 0.2 + - - -
76A GLY 3.4 0.8 - - - -
77A CYS* 1.3 76.0 - - - +
79A LEU* 1.3 61.2 + - + +
81A CYS* 4.4 5.2 - - - -
82A GLY* 2.9 26.5 + - - -
145A TRP* 3.8 26.5 - - + +
146A PHE* 3.2 26.7 - - + +
147A GLY 4.0 1.6 - - - +
148A PRO* 3.7 28.3 - - + -
151A VAL* 3.8 25.3 - - + +
257A LEU* 4.1 21.8 - - - -
258A GLY 3.9 15.9 - - - +
259A GLY 4.9 0.4 - - - +
264A ALA* 3.6 23.7 - - + +
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Residues in contact with LEU 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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75A TRP* 3.9 25.4 - - + +
76A GLY* 3.1 9.8 + - - +
78A MET* 1.3 78.4 - - + +
80A ARG* 1.3 58.2 + - - +
82A GLY 3.4 0.9 + - - -
83A GLN* 3.0 32.6 + - - +
128A ILE* 3.7 26.9 - - + -
131A MET* 3.5 34.4 - - + +
132A ALA* 4.2 18.4 - - - +
144A GLU 5.4 1.8 - - - +
146A PHE* 3.5 39.0 - - + -
151A VAL* 3.9 3.6 - - + -
154A VAL* 5.1 0.9 - - + -
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Residues in contact with ARG 80 (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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55A PHE* 3.5 23.7 - - - +
56A THR 3.0 27.8 + - - +
57A TYR* 4.2 1.3 - - + +
58A ARG* 3.5 15.3 - - - +
61A PHE* 4.2 0.4 - - - -
72A ASP* 2.8 39.8 + - - +
76A GLY 3.0 19.6 + - - +
77A CYS* 3.6 6.7 - - - +
79A LEU* 1.3 76.4 - - - +
81A CYS* 1.3 56.9 + - - +
83A GLN* 3.0 35.6 + - - +
84A MET* 3.0 32.8 + - - +
118A PHE 4.6 3.4 + - - -
120A ASP* 3.1 28.7 + - - -
128A ILE* 3.9 18.2 - - - +
280A PRO* 3.6 10.8 - - + -
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Residues in contact with CYS 81 (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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77A CYS 3.0 20.5 + - - +
78A MET* 3.7 10.1 - - - +
80A ARG* 1.3 73.0 - - - +
82A GLY* 1.3 59.6 + - - +
84A MET* 3.2 10.7 + - - +
85A MET* 2.9 24.9 + - - +
257A LEU* 3.3 24.7 - - + +
264A ALA* 3.4 19.5 - - - -
265A TYR* 3.3 31.4 - - - +
266A TYR* 3.5 9.8 - - + -
280A PRO* 3.9 10.5 - - - -
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Residues in contact with GLY 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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78A MET 2.9 15.1 + - - -
79A LEU 3.4 4.5 + - - -
81A CYS* 1.3 76.9 - - - +
83A GLN* 1.3 54.9 + - - +
85A MET* 3.4 2.4 + - - +
86A LEU* 3.0 31.2 + - - +
131A MET* 4.7 0.2 - - - -
151A VAL* 4.4 7.0 - - - -
155A LEU* 3.9 24.7 - - - +
257A LEU* 3.7 13.5 - - - +
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Residues in contact with GLN 83 (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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55A PHE* 3.5 16.9 - - + +
79A LEU 3.0 17.6 + - - +
80A ARG* 3.0 46.1 + - - +
82A GLY* 1.3 74.8 - - - +
84A MET* 1.3 58.0 + - - +
86A LEU* 3.4 0.4 + - - -
87A ALA* 2.8 32.6 + - - +
118A PHE* 3.5 38.8 + - + -
126A TYR 2.9 20.4 + - - -
127A SER 3.7 0.4 - - - -
128A ILE* 3.5 21.1 - - - +
131A MET* 3.5 16.0 - - - +
155A LEU* 5.5 0.9 - - - -
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Residues in contact with MET 84 (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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53A LEU 3.5 14.0 - - - +
54A TRP* 3.9 10.3 - - + -
55A PHE* 3.4 50.7 - - + +
80A ARG 3.0 15.2 + - - +
81A CYS* 3.2 11.6 + - - +
83A GLN* 1.3 77.2 - - - +
85A MET* 1.3 62.2 + - - +
87A ALA* 3.4 1.4 + - - +
88A GLN* 3.1 24.3 + - - +
266A TYR* 3.5 36.8 - - + -
278A LEU* 3.7 36.3 - - + +
280A PRO* 4.2 14.8 - - + -
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Residues in contact with MET 85 (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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81A CYS 2.9 16.0 + - - +
82A GLY* 3.8 4.3 - - - +
84A MET* 1.3 76.6 - - - +
86A LEU* 1.3 60.8 + - - +
88A GLN* 3.4 5.2 + - - +
89A ALA* 3.2 18.7 + - - +
155A LEU* 5.6 3.8 - - + -
224A LEU* 4.8 3.8 - - + -
226A ILE* 4.8 15.5 - - - -
254A LEU* 3.7 36.6 - - + +
256A ALA* 3.8 15.9 - - - +
257A LEU* 3.7 33.0 - - + +
266A TYR* 3.8 15.8 - - + -
319A ALA 4.1 0.9 - - - +
320A LEU 4.9 0.4 - - - -
321A GLY* 3.7 33.4 - - - +
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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
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82A GLY 3.0 17.6 + - - +
83A GLN 3.9 2.2 - - - +
85A MET* 1.3 74.0 - - - +
87A ALA* 1.3 65.7 + - - +
89A ALA* 3.1 9.0 + - + +
90A LEU* 3.0 32.0 + - + +
118A PHE* 3.9 11.0 - - + -
126A TYR* 3.5 48.2 - - + -
155A LEU* 4.0 24.2 - - + +
159A ALA* 6.3 1.3 - - + -
167A LEU* 3.8 28.7 - - + -
224A LEU* 4.0 17.7 - - + -
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Residues in contact with ALA 87 (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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53A LEU* 4.1 19.7 - - + -
55A PHE* 3.6 22.7 - - + -
83A GLN 2.8 21.7 + - - +
84A MET 3.7 4.0 - - - +
86A LEU* 1.3 71.7 - - - +
88A GLN* 1.3 57.4 + - - +
90A LEU* 3.1 5.2 + - - +
91A ILE* 2.8 35.4 + - - +
114A ILE* 4.3 0.8 - - + +
118A PHE* 3.7 19.4 - - + -
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Residues in contact with GLN 88 (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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32A LEU* 3.6 13.8 - - + +
52A ARG* 2.9 39.1 + - + +
53A LEU* 5.4 3.0 + - - +
84A MET 3.1 14.7 + - - +
85A MET 3.5 9.0 - - - +
86A LEU 3.2 0.2 - - - -
87A ALA* 1.3 76.9 - - - +
89A ALA* 1.3 55.3 + - - +
91A ILE* 3.5 6.7 + - - +
92A CYS* 3.0 47.7 + - - -
97A ARG* 3.6 14.1 - - - +
254A LEU* 3.6 16.6 - - + -
266A TYR* 3.7 16.8 - - + +
360A EDO 2.9 21.5 + - - +
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Residues in contact with ALA 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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85A MET 3.2 4.8 + - - +
86A LEU* 3.1 17.3 + - + +
88A GLN* 1.3 80.0 - - - +
90A LEU* 1.3 59.0 + - + +
92A CYS* 3.4 3.5 + - - +
93A ARG* 2.9 29.7 + - - +
167A LEU* 5.4 2.7 - - + -
224A LEU* 4.7 8.7 - - + -
254A LEU* 3.7 31.5 - - + +
323A PHE* 3.9 21.8 - - + -
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Residues in contact with LEU 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* 3.0 17.0 + - + +
87A ALA 3.6 5.6 - - - +
89A ALA* 1.3 72.4 - - - +
91A ILE* 1.3 66.1 + - - +
93A ARG* 3.3 4.1 + - + -
94A HIS* 3.0 29.8 + - - -
114A ILE* 3.4 23.5 - - + +
117A CYS* 5.2 4.0 - - + -
118A PHE* 4.0 24.7 - - + -
126A TYR* 4.0 22.2 - - + -
162A ASP* 4.9 0.7 - - - +
165A ASN* 3.4 43.3 - - + +
167A LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 91 (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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52A ARG* 4.6 16.4 - - - +
53A LEU* 4.0 28.9 - - + +
87A ALA 2.8 25.4 + - - +
88A GLN* 3.7 9.0 - - - +
90A LEU* 1.3 71.8 - - - +
92A CYS* 1.3 56.0 + - - +
95A LEU* 2.7 47.1 + - + +
96A GLY 3.1 16.5 + - - +
99A TRP* 4.3 20.2 - - + +
111A TYR* 4.3 15.9 - - + -
114A ILE* 3.9 22.2 - - + -
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Residues in contact with CYS 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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88A GLN* 3.0 48.4 + - - +
89A ALA* 3.7 4.0 - - - +
91A ILE* 1.3 78.0 - - - +
93A ARG* 1.3 63.1 + - - +
96A GLY* 3.1 24.8 + - - +
97A ARG* 3.9 19.7 - - + +
323A PHE* 4.0 19.4 - - + -
325A LYS* 4.8 4.9 + - - +
360A EDO 3.6 24.2 - - - +
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Residues in contact with ARG 93 (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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89A ALA 2.9 17.6 + - - +
90A LEU* 3.5 9.2 - - + +
91A ILE 3.3 0.4 - - - -
92A CYS* 1.3 77.6 - - - +
94A HIS* 1.3 93.6 + - - +
164A TRP 4.8 3.6 + - - -
165A ASN* 3.3 33.1 + - - +
166A SER* 5.4 1.8 - - - -
167A LEU* 4.9 3.5 - - + +
222A PRO* 3.5 32.0 - - + +
323A PHE* 3.4 26.2 - - + -
325A LYS* 3.0 45.8 + - + +
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Residues in contact with HIS 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 LEU 3.0 25.6 + - - +
93A ARG* 1.3 102.2 + - - +
95A LEU* 1.3 67.0 + - + +
110A GLU* 4.0 27.3 + - + +
114A ILE* 3.8 15.7 - - + -
164A TRP* 3.4 41.0 - + - -
165A ASN* 2.5 28.8 + - - -
325A LYS* 5.5 0.7 + - - -
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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
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91A ILE* 2.7 29.9 + - + +
94A HIS* 1.3 87.1 - - + +
96A GLY* 1.3 57.5 + - - +
99A TRP* 3.5 63.0 - - + +
108A PRO* 3.6 32.5 - - + -
110A GLU* 4.0 15.9 - - + +
111A TYR* 4.1 15.9 - - + +
114A ILE* 4.8 1.1 - - + -
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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