Contacts of the helix formed by residues 82 - 99 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 1.3 73.1 - - - +
83A PRO* 1.4 64.2 - - - +
85A MET* 3.0 29.0 + - - +
86A THR* 3.1 10.2 + - - -
108A GLN* 5.2 1.0 + - - -
121A GLN 3.2 16.3 + - - -
123A LEU* 3.7 29.3 - - - +
125A SER* 5.1 2.8 + - - -
97B LEU* 5.6 0.2 - - - -
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Residues in contact with PRO 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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81A LEU 3.2 7.2 - - - +
82A GLY* 1.4 79.5 - - - +
84A GLY* 1.3 65.1 + - - +
86A THR* 3.3 11.6 + - - +
87A ASN* 3.0 28.8 + - - -
121A GLN* 4.1 9.0 - - + +
123A LEU* 5.2 0.4 - - + -
90B THR* 3.9 5.8 - - + -
93B ALA* 5.6 0.4 - - + -
97B LEU* 5.8 0.2 - - + -
435B CYS* 3.4 42.5 - - - +
436B SER 4.0 1.3 - - - +
437B SER* 3.5 37.5 - - - +
600B TP9 3.7 11.4 - - + +
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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
----------------------------------------------------------
57A GLU* 3.7 21.1 - - - +
79A ALA* 3.3 15.5 - - - +
80A THR* 3.5 20.3 - - - +
81A LEU 3.1 6.5 + - - -
83A PRO* 1.3 80.4 - - - +
85A MET* 1.3 57.4 + - - +
87A ASN* 3.6 2.6 - - - +
88A LEU 2.9 24.6 + - - -
600B TP9 3.9 2.5 - - - +
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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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79A ALA* 4.3 6.3 - - - -
80A THR 3.1 14.2 + - - +
81A LEU* 4.9 0.4 - - - -
82A GLY* 3.0 20.5 + - - +
84A GLY* 1.3 75.5 - - - +
86A THR* 1.3 72.0 + - + +
88A LEU* 3.3 5.3 + - + +
89A SER* 2.9 25.8 + - - -
92A ILE* 5.1 2.1 - - + +
106A ALA* 3.9 8.5 - - + -
107A ALA 5.4 0.2 - - - +
123A LEU* 3.9 14.8 - - + -
125A SER* 3.6 36.6 - - - +
128A ILE* 4.0 15.0 - - + -
129A VAL* 3.9 20.4 - - + -
165A PHE* 3.9 24.0 - - + -
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Residues in contact with THR 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 3.1 2.8 + - - +
83A PRO* 3.3 16.3 - - - +
84A GLY 3.4 0.2 - - - -
85A MET* 1.3 84.8 - - + +
87A ASN* 1.3 61.4 + - - +
89A SER* 2.6 25.3 + - - -
90A THR* 4.0 2.1 + - - -
123A LEU* 3.7 21.8 - - + -
128A ILE* 4.9 1.8 - - + -
86B THR 4.1 6.2 - - - +
89B SER* 3.9 9.4 - - - +
90B THR* 2.8 31.1 + - - -
93B ALA* 4.4 4.3 - - + +
132B MET* 3.6 31.0 - - + -
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Residues in contact with ASN 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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56A HIS* 3.4 31.9 + - + -
57A GLU* 3.1 30.2 + - + +
58A PHE* 3.8 15.9 + - - +
83A PRO 3.0 15.3 + - - +
84A GLY 3.6 1.1 - - - +
86A THR* 1.3 73.5 + - - +
88A LEU* 1.3 64.1 + - - +
89A SER 3.3 0.3 + - - -
90A THR* 3.5 14.3 + - - -
56B HIS* 5.6 1.9 - - - -
58B PHE* 5.2 5.3 - - - +
87B ASN 5.4 0.2 - - - +
90B THR* 2.7 31.8 + - - +
437B SER* 4.6 3.2 + - - -
438B PHE* 4.4 2.6 + - - -
600B TP9 3.2 21.8 - - - +
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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
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57A GLU* 3.5 30.2 - - + +
60A ALA* 4.6 1.3 - - + -
61A GLY* 4.1 3.4 - - - +
77A CYS* 3.7 31.0 - - + -
78A TRP 4.4 9.2 - - - +
79A ALA* 3.8 11.2 - - + +
84A GLY 2.9 16.3 + - - +
85A MET* 3.3 6.3 + - + +
87A ASN* 1.3 75.3 - - - +
89A SER* 1.3 57.4 + - - +
91A GLY* 2.8 23.0 + - - -
92A ILE* 3.0 18.3 + - + +
104A ALA* 4.1 21.8 - - + -
105A LEU 3.8 23.1 - - - +
106A ALA* 4.9 4.7 - - + -
165A PHE* 5.3 1.3 - - + -
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Residues in contact with SER 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* 2.9 15.7 + - - -
86A THR* 2.6 23.2 + - - -
87A ASN 3.1 1.2 - - - -
88A LEU* 1.3 77.2 - - - +
90A THR* 1.3 52.4 + - - +
92A ILE* 3.6 13.9 - - - +
93A ALA* 2.7 31.5 + - - +
128A ILE* 5.4 5.1 - - - +
129A VAL* 4.9 7.0 - - - -
132A MET* 3.4 25.7 - - - +
86B THR* 3.9 16.5 + - - +
89B SER* 4.2 3.6 + - - -
128B ILE* 5.9 0.3 - - - +
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Residues in contact with THR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 3.5 28.3 - - + -
86A THR 4.5 0.7 + - - -
87A ASN* 3.5 9.8 + - - -
88A LEU 3.1 1.2 + - - -
89A SER* 1.3 77.7 + - - +
91A GLY* 1.3 57.2 + - - +
93A ALA* 3.6 2.8 + - - +
94A THR* 3.0 29.8 + - - -
435A CYS* 4.5 0.5 - - - -
437A SER* 3.8 12.6 - - - +
83B PRO* 3.9 11.4 - - + -
86B THR* 2.8 27.6 + - - +
87B ASN* 2.7 35.2 + - - +
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Residues in contact with GLY 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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58A PHE* 3.9 13.4 - - - +
61A GLY* 4.1 31.0 - - - +
62A VAL* 4.3 0.9 - - - -
87A ASN 4.3 0.8 + - - -
88A LEU 2.8 9.0 + - - -
90A THR* 1.3 76.7 - - - +
92A ILE* 1.3 58.3 + - - +
94A THR* 3.2 11.2 + - - +
95A SER* 3.1 25.5 + - - -
102A VAL* 6.1 0.6 - - - +
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Residues in contact with ILE 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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77A CYS* 5.5 1.6 - - - -
85A MET* 5.1 1.8 - - + +
88A LEU* 3.0 21.7 + - + +
89A SER* 3.2 21.5 + - - +
91A GLY* 1.3 73.9 - - - +
93A ALA* 1.3 64.7 + - - +
95A SER* 3.1 3.9 + - - -
96A VAL* 3.0 20.6 + - - +
102A VAL* 6.2 1.3 - - + -
104A ALA* 3.8 31.2 - - + -
129A VAL* 4.0 31.6 - - + -
132A MET* 3.5 29.4 - - + +
133A SER* 4.6 1.1 - - - -
163A PRO* 3.4 21.2 - - + +
165A PHE* 4.3 6.7 - - + -
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Residues in contact with ALA 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 SER 2.7 19.6 + - - +
90A THR* 3.7 8.5 - - - +
92A ILE* 1.3 73.0 - - - +
94A THR* 1.3 62.7 + - - +
96A VAL* 3.5 11.0 - - - +
97A LEU* 3.1 26.9 + - - +
132A MET* 3.9 6.0 - - - -
435A CYS* 3.8 12.3 - - - +
86B THR* 4.4 6.1 - - + +
123B LEU* 3.7 31.6 - - + -
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Residues in contact with THR 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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58A PHE* 4.0 6.4 - - - -
62A VAL* 4.0 22.9 - - + +
65A ASP* 3.9 20.2 - - - +
90A THR 3.0 18.1 + - - -
91A GLY* 3.3 12.8 - - - +
92A ILE 3.2 0.2 - - - -
93A ALA* 1.3 75.4 - - - +
95A SER* 1.3 57.5 + - - +
98A ASP* 2.9 52.6 + - - +
432A SER* 4.6 1.6 + - - +
435A CYS* 3.7 18.6 - - - +
437A SER* 4.5 3.5 - - - -
440A TYR* 4.1 10.5 - - + -
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Residues in contact with SER 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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61A GLY 5.6 0.2 - - - -
65A ASP* 3.4 12.3 - - - -
91A GLY 3.1 13.2 + - - -
92A ILE* 3.1 8.0 + - - -
94A THR* 1.3 78.6 - - - +
96A VAL* 1.3 55.6 + - - +
99A ARG* 2.9 23.2 + - - -
100A SER* 2.6 42.4 + - - -
102A VAL* 3.7 13.5 - - - +
162A GLY* 3.9 2.6 - - - -
163A PRO* 3.3 20.8 - - - +
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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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92A ILE 3.0 9.9 + - - +
93A ALA* 3.5 15.9 - - - +
95A SER* 1.3 76.9 - - - +
97A LEU* 1.3 63.7 + - - +
99A ARG* 2.9 31.2 + - - +
132A MET 3.2 34.1 - - - +
133A SER* 4.2 6.3 - - - +
134A LYS* 4.9 9.0 - - + -
161A VAL 4.5 1.4 - - - +
162A GLY* 4.5 1.6 - - - -
163A PRO* 3.5 16.5 - - + +
117B ASN* 3.7 35.7 - - + +
123B LEU* 4.2 7.9 - - + -
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Residues in contact with LEU 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 ALA 3.1 11.8 + - - +
96A VAL* 1.3 79.9 - - + +
98A ASP* 1.3 61.0 + - - +
99A ARG* 3.4 7.0 - - - +
299A ALA* 3.5 28.3 - - + +
434A GLY* 3.8 18.8 - - - +
435A CYS* 3.5 28.9 - - + +
82B GLY* 5.7 0.4 - - - -
117B ASN* 3.7 27.6 - - - +
118B ASP 4.1 0.4 - - - +
119B THR 3.5 24.7 - - - +
121B GLN* 4.0 13.9 - - - -
122B CYS 4.0 3.1 - - - +
123B LEU* 3.8 30.5 - - + -
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Residues in contact with ASP 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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65A ASP* 4.0 2.7 - - - +
69A ARG* 3.0 33.6 + - - +
94A THR* 2.9 31.2 + - - +
97A LEU* 1.3 73.0 - - - +
99A ARG* 1.3 71.7 - - - +
225A ALA* 5.9 0.5 - - - +
229A ARG* 4.8 2.4 + - - -
252A ILE* 5.1 6.8 - - + +
431A THR 4.8 1.0 - - - +
432A SER* 2.7 31.1 + - - -
433A ALA 4.3 1.6 - - - -
434A GLY 3.0 12.6 + - - +
435A CYS 2.9 28.7 + - - -
440A TYR* 4.1 5.4 + - - -
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Residues in contact with ARG 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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69A ARG* 3.5 9.9 + - - +
95A SER 2.9 9.1 + - - -
96A VAL* 2.9 21.7 + - - +
97A LEU* 3.8 6.2 + - - +
98A ASP* 1.3 84.4 - - - +
100A SER* 1.3 57.1 + - - +
160A PRO* 4.0 26.2 - - - +
161A VAL* 3.2 38.0 + - + +
229A ARG* 3.8 27.5 + - - +
297A ASP* 2.7 43.8 + - - +
299A ALA* 3.6 11.5 - - - +
300A GLU* 6.5 0.2 - - + -
117B ASN* 2.8 31.6 + - - +
118B ASP* 3.2 15.2 + - - -
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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
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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