Contacts of the helix formed by residues 92 - 110 (chain B) in PDB entry 6H25
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 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ARG 3.8 13.8 - - - +
89B ARG* 3.9 6.4 - - - +
90B PRO 3.1 5.3 - - - -
91B HIS* 1.3 78.2 - - - +
93B ASP* 1.3 63.1 + - - +
94B ARG 3.4 3.8 + - - -
95B LYS* 4.1 9.2 + - - +
96B SER* 4.5 6.2 + - - -
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ARG 3.8 8.0 + - - +
90B PRO* 6.0 0.2 - - + -
91B HIS* 3.7 4.2 - - - +
92B GLY* 1.3 76.1 - - - +
94B ARG* 1.3 66.1 + - - +
95B LYS 3.4 0.4 - - - -
96B SER* 3.4 8.1 + - - +
97B CYS* 2.8 38.1 + - - -
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE 4.4 10.7 + - - -
79A ASN* 5.2 5.3 + - - -
99A LEU* 5.8 5.7 - - - +
100A VAL* 4.0 20.2 - - + +
103A ASN* 2.1 48.2 + - - +
104A ARG* 4.9 15.8 - - + +
107A GLU* 4.1 19.3 + - - -
92B GLY 3.4 2.6 - - - -
93B ASP* 1.3 78.7 - - - +
95B LYS* 1.3 66.7 + - - +
97B CYS* 3.2 12.1 + - - +
98B GLU* 3.5 9.7 + - - +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 2.9 47.7 - - - +
76B TYR* 6.0 3.6 - - + -
92B GLY 4.1 7.3 + - - +
93B ASP 3.4 0.2 - - - -
94B ARG* 1.3 79.6 - - - +
96B SER* 1.3 63.2 + - - +
98B GLU* 3.6 9.3 + - - +
99B MET* 3.3 31.1 + - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLN* 5.9 0.2 - - - +
76B TYR* 2.8 46.9 + - - +
77B SER* 5.7 0.4 - - - -
89B ARG 6.0 0.7 - - - -
92B GLY 4.5 4.1 + - - -
93B ASP* 3.4 14.3 + - - -
94B ARG 3.3 0.4 - - - -
95B LYS* 1.3 79.0 - - - +
97B CYS* 1.3 66.4 + - - +
99B MET* 3.0 2.5 + - - +
100B GLY* 2.9 21.5 + - - -
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Residues in contact with CYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A SER* 6.5 1.1 - - - -
100A VAL* 3.7 32.1 - - + -
93B ASP* 2.8 39.3 + - - +
94B ARG* 3.2 1.3 + - - +
96B SER* 1.3 75.6 + - - +
98B GLU* 1.3 57.5 + - - +
100B GLY* 3.5 1.7 + - - -
101B LEU* 3.1 34.0 + - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.8 13.1 - - + +
101A LYS* 5.9 4.7 - - - +
104A ARG* 3.2 42.2 + - + +
108A ARG* 3.9 18.1 + - - -
235A GLN* 4.0 7.5 + - - +
94B ARG 3.5 7.6 + - - +
95B LYS* 3.7 11.2 - - - +
96B SER 3.2 0.2 - - - -
97B CYS* 1.3 78.2 - - - +
99B MET* 1.3 66.5 + - - +
101B LEU* 3.1 5.5 + - + +
102B GLN* 3.0 58.3 + - + +
200B GLU* 4.5 0.2 - - - +
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Residues in contact with MET 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.6 48.0 - - + +
95B LYS* 3.3 21.7 + - + +
96B SER 3.0 8.3 + - - +
98B GLU* 1.3 86.4 - - - +
100B GLY* 1.3 60.6 + - - +
102B GLN* 4.0 8.2 + - - +
103B LEU* 3.3 32.2 + - + +
134B THR* 5.9 4.3 - - + -
135B TYR* 3.6 43.5 - - + +
138B CYS* 5.7 0.7 - - - -
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Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B CYS* 3.7 23.5 - - - +
75B GLN* 4.9 0.4 - - - -
76B TYR* 4.0 14.0 - - - +
96B SER 2.9 14.7 + - - -
97B CYS* 3.9 2.7 - - - -
99B MET* 1.3 77.2 - - - +
101B LEU* 1.3 59.7 + - - +
103B LEU* 3.2 8.2 + - - +
104B ARG* 2.9 24.5 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 3.8 47.1 - - + +
100A VAL* 4.9 7.2 - - + -
101A LYS* 5.2 7.0 - - + -
74B CYS 6.1 0.2 - - - +
97B CYS* 3.1 23.9 + - + +
98B GLU* 3.1 8.7 + - + +
100B GLY* 1.3 77.5 - - - +
102B GLN* 1.3 60.1 + - + +
104B ARG* 3.3 46.0 + - - +
105B GLN* 2.9 25.5 + - - +
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLN* 3.4 14.2 - - - +
236A SER 5.8 0.9 - - - +
98B GLU* 3.0 47.4 + - + +
99B MET* 4.4 7.7 - - - +
101B LEU* 1.3 75.9 - - + +
103B LEU* 1.3 61.3 + - - +
105B GLN* 3.2 15.4 + - - +
106B THR* 2.9 33.4 + - - +
135B TYR* 4.0 26.6 - - + +
198B LEU* 4.7 7.4 - - + +
200B GLU* 2.4 42.8 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B CYS* 3.8 16.8 - - + -
76B TYR* 5.9 4.3 - - + -
99B MET* 3.3 23.0 + - + +
100B GLY* 3.2 10.7 + - - +
102B GLN* 1.3 76.2 - - - +
104B ARG* 1.3 58.6 + - - +
106B THR* 3.0 5.0 + - - +
107B PHE* 2.9 61.9 + - + +
123B ILE* 5.4 1.8 - - + -
125B VAL* 5.1 11.0 - - + -
135B TYR* 3.7 29.2 - - + -
138B CYS* 4.7 11.4 - - + +
139B VAL* 4.1 15.7 - - + -
142B ALA* 4.4 12.8 - - + -
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Residues in contact with ARG 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 3.6 20.2 + - - -
72B VAL* 3.7 26.8 + - + +
73B ASN* 4.1 17.6 + - - -
74B CYS* 3.8 21.6 + - + +
100B GLY 2.9 13.3 + - - +
101B LEU* 3.4 37.1 - - - +
102B GLN 3.3 0.2 - - - -
103B LEU* 1.3 76.6 - - - +
105B GLN* 1.3 56.2 + - - +
107B PHE 3.7 0.5 - - - -
108B GLU* 2.9 40.9 + - - +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 3.2 21.7 + - - +
237A SER* 3.3 32.9 - - - +
238A GLY 3.7 2.6 + - - +
239A GLY* 3.4 29.3 - - - +
240A ILE 4.6 1.4 - - - +
101B LEU 2.9 13.5 + - - +
102B GLN* 3.2 15.6 + - - +
104B ARG* 1.3 77.0 - - - +
106B THR* 1.3 59.6 + - + +
108B GLU* 3.3 4.6 + - - +
109B ALA* 3.0 27.6 + - + +
197B ALA 4.3 6.7 + - - +
198B LEU* 3.6 24.6 - - + +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN 2.9 16.9 + - - +
103B LEU* 3.0 17.7 + - - +
105B GLN* 1.3 76.7 - - + +
107B PHE* 1.3 77.5 + - - +
109B ALA* 3.3 20.7 + - - +
110B ALA* 3.7 6.9 + - - +
135B TYR* 3.4 21.8 + - - +
139B VAL* 4.8 6.4 - - + +
157B VAL* 5.6 9.9 - - - +
188B ALA* 4.6 9.0 - - + -
197B ALA* 5.0 9.2 - - + +
198B LEU* 3.7 24.2 - - + -
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 3.7 14.9 - - + +
74B CYS* 4.8 0.2 - - - -
103B LEU* 2.9 40.6 + - + +
104B ARG 3.7 1.3 - - - -
106B THR* 1.3 100.4 - - - +
108B GLU* 1.3 59.6 + - - +
109B ALA 3.3 0.7 - - - -
110B ALA 4.5 4.5 - - - +
111B ILE* 3.3 45.9 - - + +
123B ILE* 3.8 25.8 - - + -
139B VAL* 4.0 10.8 - - + -
142B ALA* 3.6 20.9 - - + -
143B THR* 3.5 32.1 - - - -
146B VAL* 4.3 10.8 - - + -
153B MET* 4.5 11.7 - - + -
157B VAL* 5.2 5.6 - - + -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLY* 5.5 2.6 - - - +
66B LEU* 5.5 3.3 - - - +
69B ARG* 3.9 30.8 + - - +
70B ALA 5.2 2.2 - - - +
72B VAL* 4.7 13.0 - - + +
104B ARG* 2.9 30.7 + - - +
105B GLN* 3.8 3.8 - - - +
107B PHE* 1.3 76.6 - - - +
109B ALA* 1.3 65.6 + - - +
110B ALA* 3.6 0.7 - - - -
111B ILE* 4.7 6.3 + - - +
113B THR* 4.6 17.6 + - + +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLY* 4.5 21.8 - - - -
240A ILE 5.2 1.3 - - - +
241A MET* 3.5 21.7 - - + +
105B GLN* 3.0 14.0 + - + +
106B THR* 3.3 16.8 - - - +
107B PHE 3.3 0.4 - - - -
108B GLU* 1.3 81.3 - - - +
110B ALA* 1.3 52.6 + - + +
154B ARG* 2.6 29.3 + - - -
197B ALA* 5.2 10.5 - - + +
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A MET* 3.7 17.3 - - + -
106B THR 3.7 7.9 + - - +
107B PHE* 4.8 2.4 - - - -
109B ALA* 1.3 79.0 - - + +
111B ILE* 1.3 62.2 + - - +
112B LEU 3.8 0.2 - - - -
153B MET* 3.3 24.9 - - - +
154B ARG* 3.6 28.9 - - + +
155B ASP 4.8 3.1 - - - +
157B VAL* 4.9 12.2 - - + +
190B LEU* 4.6 7.0 - - + -
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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