Contacts of the helix formed by residues 82 - 99 (chain B) in PDB entry 2IHU
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 5.7 0.2 - - - -
81B LEU* 1.3 73.9 - - - +
83B PRO* 1.3 63.9 - - - +
85B MET* 3.0 29.1 + - - +
86B THR* 3.1 10.7 + - - -
108B GLN* 5.2 0.8 + - - -
121B GLN 3.3 16.5 + - - -
123B LEU* 3.6 28.3 - - - +
125B SER* 5.1 2.8 + - - -
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.9 5.4 - - + -
97A LEU* 5.7 0.2 - - + -
435A CYS* 3.3 44.9 - - - +
436A SER 4.0 3.4 - - - +
437A SER* 3.5 37.9 - - - +
600A TP9 3.8 7.2 - - + +
81B LEU 3.2 6.7 - - - +
82B GLY* 1.3 78.9 - - - +
84B GLY* 1.3 59.5 + - - +
86B THR* 3.2 12.3 + - - +
87B ASN* 3.0 33.8 + - - -
121B GLN* 4.1 9.0 - - + +
123B LEU* 4.4 1.1 - - + -
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A TP9 3.9 2.5 - - - +
57B GLU* 3.7 20.8 - - - +
79B ALA* 3.3 16.0 - - - +
80B THR* 3.6 20.3 - - - +
81B LEU 3.2 4.8 + - - -
82B GLY 3.2 1.4 - - - -
83B PRO* 1.3 81.7 - - - +
85B MET* 1.3 56.7 + - - +
87B ASN* 3.5 2.6 - - - +
88B LEU 2.9 24.1 + - - -
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 4.3 6.7 - - - -
80B THR 3.0 15.4 + - - +
81B LEU* 4.7 0.4 - - - -
82B GLY* 3.0 20.5 + - - +
84B GLY* 1.3 74.7 - - - +
86B THR* 1.3 73.4 + - + +
88B LEU* 3.2 5.4 + - + +
89B SER* 2.9 25.6 + - - -
92B ILE* 5.2 1.5 - - + +
106B ALA* 3.9 8.7 - - + -
123B LEU* 3.9 9.2 - - + -
125B SER* 3.5 28.9 - - - +
128B ILE* 3.9 26.5 - - + -
129B VAL* 3.8 22.4 - - + -
165B PHE* 3.8 24.0 - - + -
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR 4.1 7.1 - - - +
89A SER* 3.9 9.0 - - - +
90A THR* 2.8 30.8 + - - -
93A ALA* 4.4 3.8 - - + +
132A MET* 3.7 24.2 - - + -
82B GLY 3.1 5.9 + - - -
83B PRO* 3.2 18.9 - - - +
85B MET* 1.3 85.9 - - + +
87B ASN* 1.3 59.6 - - - +
89B SER* 2.7 25.0 + - - +
90B THR* 4.0 2.4 + - - -
123B LEU* 3.6 29.8 - - + -
128B ILE* 4.9 1.8 - - + -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 5.7 1.7 - - - -
58A PHE* 5.2 4.4 - - - +
87A ASN* 5.4 0.2 - - - +
90A THR* 2.7 32.3 + - - +
437A SER* 4.5 3.6 + - - -
438A PHE* 4.4 3.0 + - - -
600A TP9 3.2 20.8 - - - +
56B HIS* 3.4 29.7 + - + -
57B GLU* 3.0 31.9 + - + +
58B PHE* 3.8 16.3 + - - +
83B PRO 3.0 16.5 + - - +
84B GLY 3.5 2.0 - - - +
86B THR* 1.3 76.1 - - - +
88B LEU* 1.3 60.5 - - - +
89B SER 3.4 0.5 + - - -
90B THR* 3.6 13.1 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.5 30.7 - - + +
60B ALA* 4.6 1.1 - - + -
61B GLY* 4.1 6.3 - - - +
77B CYS* 3.8 26.5 - - + -
78B TRP 4.3 10.1 - - - +
79B ALA* 3.9 16.2 - - + +
84B GLY 2.9 13.9 + - - +
85B MET* 3.2 9.4 + - + +
87B ASN* 1.3 76.9 - - - +
89B SER* 1.3 57.1 + - - +
91B GLY* 2.9 19.8 + - - -
92B ILE* 2.9 19.1 + - + +
104B ALA* 4.1 22.4 - - + -
105B LEU 4.0 16.6 - - - +
106B ALA* 5.0 4.9 - - + -
165B PHE* 5.3 1.3 - - + -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.9 13.8 - - - +
89A SER* 4.2 5.2 + - - -
128A ILE* 5.7 1.2 - - - +
85B MET* 2.9 13.7 + - - -
86B THR* 2.7 23.4 + - - -
87B ASN 3.2 0.6 - - - -
88B LEU* 1.3 75.9 - - - +
90B THR* 1.3 57.0 + - - +
91B GLY 3.3 0.2 - - - -
92B ILE* 3.6 13.5 - - - -
93B ALA* 2.8 29.7 + - - +
128B ILE* 5.4 5.0 - - - +
129B VAL* 4.8 8.1 - - - -
132B MET* 3.4 23.8 - - - +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 3.9 13.0 - - + -
86A THR* 2.8 30.5 + - - +
87A ASN* 2.7 31.8 + - - +
58B PHE* 3.6 26.7 - - + -
86B THR 4.4 0.9 + - - -
87B ASN* 3.6 10.3 + - - -
88B LEU 3.2 1.0 - - - -
89B SER* 1.3 78.3 + - - +
91B GLY* 1.3 57.1 + - - +
93B ALA* 3.6 3.4 + - - +
94B THR* 3.0 28.8 + - - -
435B CYS* 4.5 0.5 - - - -
437B SER* 3.9 11.2 - - - +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 3.9 7.4 - - - +
61B GLY* 4.1 30.3 - - - +
62B VAL* 4.3 7.2 - - - -
65B ASP* 5.1 0.2 - - - +
87B ASN 4.4 1.0 + - - -
88B LEU 2.9 9.4 + - - -
90B THR* 1.3 76.8 - - - +
92B ILE* 1.3 63.1 + - - +
94B THR* 3.3 10.3 + - - +
95B SER* 3.1 21.7 + - - -
102B VAL* 6.1 1.1 - - - +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY* 5.2 0.2 - - - -
77B CYS* 5.4 1.8 - - - -
85B MET* 5.2 1.6 - - + +
88B LEU* 2.9 25.5 + - + +
89B SER* 3.4 19.3 + - - +
91B GLY* 1.3 76.0 - - - +
93B ALA* 1.3 57.2 + - - +
95B SER* 3.1 3.6 + - - -
96B VAL* 2.9 25.1 + - - +
102B VAL* 6.1 2.2 - - + -
104B ALA* 3.7 30.5 - - + -
129B VAL* 3.9 28.9 - - + -
132B MET* 3.5 29.4 - - + +
133B SER* 4.6 1.6 - - - -
163B PRO* 3.4 22.0 - - + +
165B PHE* 4.2 9.4 - - + -
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Residues in contact with ALA 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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83A PRO* 5.6 0.2 - - + -
86A THR* 4.4 5.4 - - + +
123A LEU* 3.7 31.4 - - + -
89B SER 2.8 20.6 + - - +
90B THR* 3.7 9.9 - - - +
92B ILE* 1.3 72.5 - - - +
94B THR* 1.3 61.7 + - - +
96B VAL* 3.3 11.6 - - - +
97B LEU* 3.1 27.7 + - - +
132B MET* 4.0 5.4 - - - -
435B CYS* 3.9 11.2 - - - +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 4.0 5.7 - - - -
62B VAL* 3.9 18.1 - - + +
65B ASP* 4.0 15.0 - - + +
90B THR 3.0 16.0 + - - -
91B GLY 3.4 10.5 - - - -
93B ALA* 1.3 75.3 - - - +
95B SER* 1.3 56.4 + - - +
98B ASP* 2.8 54.3 + - - +
432B SER* 4.2 2.6 + - - +
435B CYS* 3.6 17.8 - - - +
437B SER* 4.5 3.5 - - - -
440B TYR* 4.0 21.6 - - + -
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 3.5 13.4 + - - -
91B GLY 3.1 12.7 + - - -
92B ILE* 3.1 8.0 + - - -
94B THR* 1.3 77.6 - - - +
96B VAL* 1.3 57.5 + - - +
99B ARG* 3.0 21.0 + - - -
100B SER* 2.6 43.2 + - - -
102B VAL* 3.7 13.2 - - - +
162B GLY* 3.8 2.8 - - - -
163B PRO* 3.2 21.6 - - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.8 35.0 - - + +
123A LEU* 4.0 10.1 - - + -
92B ILE 2.9 6.8 + - - +
93B ALA* 3.3 19.1 - - - +
95B SER* 1.3 76.3 - - - +
97B LEU* 1.3 63.6 + - - +
99B ARG* 2.9 29.6 + - - +
132B MET 3.3 36.8 - - - +
133B SER* 4.0 7.0 - - - +
134B LYS* 5.0 7.9 - - + -
161B VAL 4.4 1.9 - - - +
162B GLY* 4.5 1.6 - - - -
163B PRO* 3.5 12.8 - - + -
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Residues in contact with LEU 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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82A GLY* 5.6 0.4 - - - -
117A ASN* 3.7 27.6 - - - +
118A ASP 4.1 0.2 - - - +
119A THR 3.5 22.9 - - - +
121A GLN* 4.1 2.2 - - - -
122A CYS 4.0 13.0 - - - +
123A LEU* 3.6 32.5 - - + -
93B ALA 3.1 14.0 + - - +
96B VAL* 1.3 78.1 - - - +
98B ASP* 1.3 63.4 + - - +
99B ARG* 3.3 8.3 + - - +
299B ALA* 3.5 29.2 - - + +
434B GLY* 3.7 31.0 - - - +
435B CYS* 3.7 13.9 - - + +
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Residues in contact with ASP 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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65B ASP* 4.3 0.6 - - - +
69B ARG* 3.2 25.1 + - - +
94B THR* 2.8 33.9 + - - +
97B LEU* 1.3 69.9 - - - +
99B ARG* 1.3 74.8 + - - +
225B ALA* 5.9 1.0 - - - +
229B ARG* 4.8 2.4 + - - -
252B ILE* 5.2 5.8 - - + +
431B THR 4.8 0.6 - - - +
432B SER* 2.4 29.9 + - - -
433B ALA 4.1 4.7 - - - -
434B GLY 2.9 12.2 + - - +
435B CYS 2.8 30.2 + - - -
440B TYR* 4.2 4.2 + - - -
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Residues in contact with ARG 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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117A ASN* 2.7 25.4 + - - +
118A ASP* 3.2 22.4 + - - -
69B ARG* 3.5 9.0 + - - +
95B SER 3.0 12.9 + - - -
96B VAL* 2.9 21.5 + - - +
97B LEU 3.3 6.8 + - - +
98B ASP* 1.3 86.0 - - - +
100B SER* 1.3 62.1 + - - +
160B PRO* 3.9 26.8 - - - +
161B VAL* 3.2 32.7 - - + +
229B ARG* 3.8 26.2 + - - +
297B ASP* 2.7 44.3 + - - +
299B ALA* 3.6 11.8 - - - +
300B GLU* 6.5 0.4 - - + -
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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