Contacts of the helix formed by residues 80 - 99 (chain A) in PDB entry 4R0C
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 PHE 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASN 3.3 11.6 + - - +
77A PHE* 2.9 16.9 + - + +
78A THR 3.4 1.4 - - - +
79A GLY* 1.3 76.5 - - - +
81A ALA* 1.3 67.4 + - - +
82A PRO* 3.4 24.7 - - + -
83A LEU* 3.1 19.2 + - + +
84A GLY 4.2 2.8 + - - -
186A LEU* 3.7 23.8 - - + -
189A GLU* 3.4 36.3 - - + -
341A MET* 3.9 20.4 - - + -
344A ALA* 3.9 8.5 - - + -
345A ALA* 3.5 45.5 - - + -
348A VAL* 4.3 13.2 - - + -
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Residues in contact with ALA 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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79A GLY 3.2 4.1 + - - -
80A PHE* 1.3 71.2 - - - +
82A PRO* 1.4 64.4 - - - +
83A LEU 3.3 0.7 + - - -
84A GLY* 4.3 2.1 + - - -
85A VAL* 3.7 17.2 + - - +
185A GLY* 3.3 28.4 - - - +
188A THR* 4.2 13.7 - - + -
189A GLU* 2.7 22.5 + - + +
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Residues in contact with PRO 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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80A PHE* 3.4 37.2 - - + -
81A ALA* 1.4 95.0 - - + +
83A LEU* 1.3 57.4 + - - +
85A VAL* 4.6 2.7 - - + -
86A VAL* 3.2 15.1 + - - +
181A ALA 4.3 6.3 - - - +
182A THR* 3.7 22.7 - - + +
185A GLY* 3.7 15.0 - - - +
186A LEU* 3.9 9.4 - - + +
189A GLU* 4.3 0.9 - - + -
337A TYR* 2.6 29.6 + - - +
341A MET* 3.8 9.0 - - - -
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Residues in contact with LEU 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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77A PHE* 3.9 39.3 - - + +
78A THR* 4.3 13.2 - - - +
80A PHE* 3.1 16.2 + - + +
81A ALA 3.2 0.2 - - - -
82A PRO* 1.3 79.2 - - - +
84A GLY* 1.3 71.8 + - - +
86A VAL* 3.3 4.7 + - - +
87A LEU* 3.1 39.2 + - + +
337A TYR* 4.2 8.1 - - + -
338A LEU* 3.7 29.4 - - + -
341A MET* 3.8 27.8 - - + -
78B THR* 5.5 2.9 - - + -
83B LEU* 6.6 0.2 - - + -
87B LEU* 6.3 0.7 - - + -
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Residues in contact with GLY 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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78A THR 5.2 0.2 + - - -
80A PHE 4.2 4.2 + - - -
81A ALA 4.3 1.4 + - - -
83A LEU* 1.3 82.1 - - - +
85A VAL* 1.3 62.5 + - - +
87A LEU* 3.2 9.2 + - - +
88A VAL* 3.1 26.0 + - - +
74B VAL* 3.5 7.4 - - - -
77B PHE* 5.2 1.1 - - - -
78B THR* 3.5 29.5 - - - +
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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
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81A ALA 3.7 20.6 + - - +
82A PRO* 4.4 4.7 - - + +
84A GLY* 1.3 71.0 - - - +
86A VAL* 1.3 58.2 + - - +
88A VAL* 3.4 1.2 + - - +
89A ALA* 2.9 27.7 + - - +
181A ALA* 4.1 28.7 - - + +
296A VAL* 4.1 11.9 - - + -
297A VAL* 3.8 20.5 - - + +
74B VAL* 3.5 23.1 - - + +
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Residues in contact with VAL 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 PRO 3.2 23.1 - - - +
83A LEU 3.3 1.5 + - - +
84A GLY 3.2 0.8 - - - -
85A VAL* 1.3 80.9 - - - +
87A LEU* 1.3 59.5 + - - +
89A ALA* 3.2 6.9 + - - +
90A MET* 2.9 39.0 + - + +
178A PRO* 3.6 19.1 - - + +
181A ALA* 4.2 7.0 - - + -
182A THR* 3.2 33.2 - - - +
334A MET* 3.9 17.5 - - + -
337A TYR* 3.4 23.1 - - + +
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Residues in contact with LEU 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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83A LEU* 3.1 39.2 + - + +
84A GLY* 3.5 7.0 - - - +
86A VAL* 1.3 78.0 - - - +
88A VAL* 1.3 61.3 - - - +
90A MET* 3.2 3.1 + - - -
91A LEU* 3.1 19.6 + - - +
331A MET* 3.3 24.6 - - + +
334A MET* 4.2 35.9 - - + -
337A TYR* 4.8 2.7 - - + -
338A LEU* 4.3 26.7 - - + -
77B PHE* 4.0 28.9 - - + -
83B LEU* 6.0 1.3 - - + -
87B LEU* 6.0 0.9 - - + -
338B LEU* 5.1 8.5 - - + -
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Residues in contact with VAL 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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84A GLY 3.1 15.6 + - - +
85A VAL 3.9 3.1 - - - +
87A LEU* 1.3 72.8 - - - +
89A ALA* 1.3 66.3 + - - +
91A LEU* 3.2 21.2 + - - +
92A GLY 3.5 3.3 + - - -
297A VAL* 4.2 9.4 - - + -
806A LMT 3.5 18.7 - - + +
73B LEU* 4.1 12.1 - - + -
74B VAL* 4.1 20.9 - - + -
77B PHE* 3.9 18.6 - - + -
342B PHE* 3.6 39.5 - - + -
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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 VAL 2.9 19.2 + - - +
86A VAL* 3.2 6.9 + - - +
88A VAL* 1.3 75.2 - - - +
90A MET* 1.3 59.1 + - - +
92A GLY 3.1 3.1 + - - -
93A LEU* 2.9 27.5 + - + +
178A PRO* 4.1 14.8 - - + -
296A VAL* 4.1 25.1 - - + +
297A VAL* 4.7 5.1 - - + +
300A ALA* 3.4 22.4 - - + +
806A LMT 5.3 0.2 - - - -
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Residues in contact with MET 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 VAL* 2.9 25.4 + - + +
87A LEU 3.5 5.8 - - - +
88A VAL 3.2 0.2 - - - -
89A ALA* 1.3 74.8 - - - +
91A LEU* 1.3 58.7 + - - +
93A LEU* 4.3 7.6 - - + +
94A GLY* 2.6 41.2 + - - +
97A GLU* 5.8 0.2 - - - +
131A LEU 6.0 1.3 - - - +
133A VAL* 4.3 24.7 - - + -
178A PRO* 3.6 28.3 - - - -
330A THR* 3.3 30.8 - - + +
331A MET* 3.9 7.2 - - + -
333A SER* 5.8 1.3 - - - +
334A MET* 3.6 26.2 - - - +
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Residues in contact with LEU 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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87A LEU 3.1 8.0 + - - +
88A VAL* 3.2 14.1 + - - +
90A MET* 1.3 78.1 - - - +
92A GLY* 1.3 58.7 + - - +
94A GLY* 4.4 0.2 - - - -
95A VAL* 3.2 27.5 + - - +
327A MET* 3.9 29.8 - - + +
330A THR* 5.1 1.1 - - - -
331A MET* 3.5 38.8 - - + -
806A LMT 3.8 12.9 - - + +
77B PHE* 6.4 0.4 - - + -
338B LEU 5.9 0.4 - - - +
339B VAL* 3.8 15.9 - - + -
342B PHE* 3.5 49.8 - - + -
343B PHE* 4.7 1.8 - - + -
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Residues in contact with GLY 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 VAL 3.5 3.2 + - - -
89A ALA 3.1 6.2 + - - -
91A LEU* 1.3 78.7 - - - +
93A LEU* 1.3 61.2 + - - +
95A VAL 3.4 1.6 + - - -
96A ALA 3.3 9.4 + - - -
300A ALA 3.5 20.6 - - - -
304A GLY* 3.1 22.4 + - - -
806A LMT 3.8 24.1 - - - +
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Residues in contact with LEU 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 16.2 + - + +
90A MET* 4.3 12.6 - - + +
92A GLY* 1.3 72.8 - - - +
94A GLY* 1.3 66.4 + - - +
96A ALA* 3.0 6.2 + - - +
97A GLU* 2.9 24.7 + - - +
102A LEU* 4.4 12.8 - - + +
131A LEU* 4.0 34.8 - - + +
177A GLY* 5.1 1.3 - - - -
178A PRO* 3.5 39.0 - - + -
296A VAL 5.6 0.7 - - - +
299A VAL* 5.2 3.6 - - + +
300A ALA* 3.8 18.4 - - + +
303A ALA* 3.7 24.2 - - + -
803A BOG 6.0 0.7 - - + -
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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 MET* 2.6 25.9 + - - +
91A LEU 4.4 0.2 - - - -
93A LEU* 1.3 73.1 - - - +
95A VAL* 1.3 59.9 + - - +
97A GLU* 3.4 5.9 + - - +
98A GLN* 3.1 31.1 + - - +
326A ALA 4.9 1.1 - - - -
330A THR* 3.1 29.2 - - - -
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Residues in contact with VAL 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 LEU 3.2 18.3 + - - +
92A GLY 3.4 8.4 + - - +
93A LEU 3.2 0.8 - - - -
94A GLY* 1.3 74.4 - - - +
96A ALA* 1.3 63.9 + - - +
99A SER* 3.2 23.2 + - - -
304A GLY* 3.9 9.0 - - - +
308A ALA* 3.8 22.2 - - + +
317A PHE* 3.7 11.2 - - + -
323A VAL* 3.9 24.5 - - + +
326A ALA* 4.1 15.0 - - + -
327A MET* 3.5 25.8 - - + +
806A LMT 4.5 5.4 - - + -
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Residues in contact with ALA 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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92A GLY 3.3 6.9 + - - +
93A LEU 3.0 10.4 + - - +
95A VAL* 1.3 80.8 - - - +
97A GLU* 1.3 59.7 + - - +
99A SER* 2.8 23.1 + - - -
101A LEU* 3.4 11.5 + - + +
102A LEU* 3.7 27.3 + - + -
303A ALA* 3.6 30.3 - - + +
304A GLY* 4.6 0.2 - - - -
307A GLY* 4.0 7.8 - - - -
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Residues in contact with GLU 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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90A MET* 5.8 0.3 - - - +
93A LEU 2.9 14.5 + - - +
94A GLY* 3.9 6.9 - - - +
95A VAL 3.4 0.2 - - - -
96A ALA* 1.3 76.4 - - - +
98A GLN* 1.3 57.4 + - - +
100A GLY* 2.7 28.1 + - - -
102A LEU* 3.9 12.3 - - + +
103A SER* 5.7 2.7 - - - +
131A LEU 5.0 0.2 - - - +
132A THR* 3.4 17.4 - - - +
133A VAL* 3.0 32.2 + - - +
134A ASP* 3.2 13.9 + - - +
135A ALA* 3.1 34.4 + - + +
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Residues in contact with GLN 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* 3.1 22.0 + - - +
97A GLU* 1.3 78.6 - - - +
99A SER* 1.3 60.0 + - - +
100A GLY 3.1 0.2 - - - -
316A GLN* 3.6 19.2 - - - +
317A PHE* 3.8 20.8 - - + -
326A ALA* 3.9 15.8 - - + +
329A VAL* 3.8 27.4 - - + +
330A THR* 3.6 13.5 + - - -
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Residues in contact with SER 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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95A VAL 3.2 14.1 + - - -
96A ALA 2.8 17.5 + - - -
97A GLU 3.1 0.6 - - - -
98A GLN* 1.3 77.5 - - - +
100A GLY* 1.3 60.2 + - - +
101A LEU* 3.2 16.3 + - - +
307A GLY* 3.2 26.9 + - - -
310A TYR* 3.5 14.9 - - - -
311A GLY* 3.6 9.6 - - - -
316A GLN* 3.5 20.7 - - - +
317A PHE* 3.4 14.6 - - - -
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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