Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1IS2
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 ASP 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A SER* 1.3 79.4 + - - +
82A PRO* 1.3 77.9 - - - +
83A GLU* 3.0 15.2 + - - +
84A GLU* 3.0 47.6 + - + +
85A ILE* 2.9 27.9 + - - +
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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 SER 3.2 7.6 - - - +
81A ASP* 1.3 94.3 - - - +
83A GLU* 1.3 64.0 + - + +
85A ILE* 3.5 12.6 + - + +
86A MET* 3.1 20.4 + - - +
284A PHE* 6.6 0.2 - - + -
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Residues in contact with GLU 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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24A ASP 5.3 3.7 - - - +
29A ASN* 4.6 9.9 + - - +
81A ASP* 3.0 18.0 + - - +
82A PRO* 1.3 80.9 - - + +
84A GLU* 1.3 58.3 + - + +
86A MET* 2.8 25.5 + - - +
87A TRP* 3.0 49.5 + - + +
346A ARG* 5.5 7.6 + - - -
349A LYS* 5.4 12.9 + - + +
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Residues in contact with GLU 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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32A ARG* 3.0 48.9 + - - +
36A ILE* 3.6 15.4 - - + +
78A GLY 5.5 0.5 - - - +
79A ILE* 3.8 18.6 - - + +
80A SER 5.1 0.2 + - - -
81A ASP* 3.0 31.9 + - + +
83A GLU* 1.3 75.4 - - - +
85A ILE* 1.3 57.8 + - - +
87A TRP* 3.4 20.6 + - + +
88A PHE* 2.9 30.3 + - - +
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Residues in contact with ILE 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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74A MET* 3.9 18.6 - - + +
79A ILE* 3.8 28.5 - - + +
80A SER* 3.5 20.6 - - - +
81A ASP 2.9 16.9 + - - +
82A PRO* 3.7 12.1 - - + +
83A GLU 3.1 0.2 - - - -
84A GLU* 1.3 77.2 - - - +
86A MET* 1.3 57.1 + - - +
88A PHE* 3.8 3.2 - - - +
89A LYS* 2.9 48.8 + - - +
104A LEU* 6.2 0.4 - - + -
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Residues in contact with MET 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 3.1 12.7 + - - +
83A GLU* 2.8 16.5 + - - +
85A ILE* 1.3 76.4 - - - +
87A TRP* 1.3 63.5 + - + +
89A LYS* 3.3 11.2 + - + +
90A ASN* 2.9 72.8 + - - +
284A PHE* 6.4 5.6 - - + -
288A ASN* 6.2 2.0 - - - +
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Residues in contact with TRP 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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24A ASP* 5.0 8.8 + - - -
29A ASN* 3.7 32.8 - - + -
32A ARG* 3.8 15.5 - - + -
33A ARG* 3.6 60.6 - - + +
36A ILE* 3.9 15.3 - - + -
37A GLU* 5.1 1.9 - - + +
83A GLU* 3.0 46.4 + - + -
84A GLU* 3.7 26.0 - - + +
86A MET* 1.3 80.8 - - + +
88A PHE* 1.3 63.8 + - - +
90A ASN* 3.2 11.5 + - - +
91A SER* 3.0 28.0 + - - +
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Residues in contact with PHE 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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36A ILE* 3.5 18.1 - - + +
39A LEU* 4.3 6.7 - - + -
40A ILE* 3.8 17.9 - - + -
46A PHE* 4.2 11.7 - + - -
70A MET* 4.2 11.7 - - + -
73A LYS* 4.2 7.0 - - + -
74A MET* 3.4 33.9 - - + -
77A TYR* 3.9 29.6 - + - -
79A ILE* 3.2 29.4 - - + -
84A GLU 2.9 17.7 + - - +
85A ILE 3.8 4.3 - - - +
87A TRP* 1.3 76.7 - - - +
89A LYS* 1.3 62.1 + - - +
91A SER* 3.3 4.7 + - - -
92A VAL* 3.1 38.7 + - + +
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Residues in contact with LYS 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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70A MET* 3.7 27.6 - - + -
74A MET* 4.7 1.8 - - + -
85A ILE* 2.9 36.5 + - - +
86A MET* 3.8 11.6 - - - +
88A PHE* 1.3 77.0 - - - +
90A ASN* 1.3 65.9 + - - +
93A HIS* 3.1 33.0 + - + +
98A GLU* 3.7 16.2 + - + +
101A ASP* 5.5 7.7 + - - +
104A LEU* 3.8 37.1 - - - +
105A GLY* 5.5 1.2 - - - +
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Residues in contact with ASN 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 MET* 2.9 58.2 + - - +
87A TRP* 3.5 12.2 - - - +
89A LYS* 1.3 80.3 - - - +
91A SER* 1.3 53.8 + - - +
93A HIS* 5.5 0.2 - - - -
94A ARG* 2.7 35.9 + - - -
95A GLY* 3.5 13.9 + - - +
616A THR* 5.3 5.6 - - + +
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Residues in contact with SER 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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37A GLU* 3.2 35.1 - - - +
40A ILE* 3.6 33.0 - - - +
41A LEU* 5.9 5.8 - - - +
87A TRP 3.0 13.5 + - - -
88A PHE 3.3 7.8 + - - -
90A ASN* 1.3 79.5 - - - +
92A VAL* 1.3 61.3 + - - +
94A ARG* 3.7 14.7 + - - +
615A MET* 5.7 1.7 - - - +
616A THR* 5.5 5.6 - - - -
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Residues in contact with VAL 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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40A ILE* 3.6 25.6 - - + +
46A PHE* 3.8 32.2 - - + +
66A LYS* 2.7 42.4 + - + +
70A MET* 4.3 7.2 - - + -
88A PHE* 3.1 34.7 + - + +
89A LYS 3.8 4.0 - - - +
90A ASN 3.3 0.2 - - - -
91A SER* 1.3 79.4 - - - +
93A HIS* 1.3 77.8 + - + +
94A ARG* 4.0 4.2 + - - +
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Residues in contact with HIS 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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51A TYR* 4.4 7.4 + - - -
63A ALA* 3.8 13.1 - - - -
66A LYS* 3.8 21.8 - - + +
67A SER* 3.0 33.7 + - - -
70A MET* 3.6 21.2 - - - -
89A LYS* 3.1 23.2 + - + +
90A ASN* 5.5 0.2 - - - -
92A VAL* 1.3 82.7 - - + +
94A ARG* 1.3 73.3 + - - +
95A GLY 3.3 1.1 - - - +
96A HIS* 2.9 41.9 + - + +
97A PRO 4.7 2.0 + - - -
98A GLU* 3.3 31.3 - - + +
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Residues in contact with ARG 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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46A PHE 3.7 11.5 + - - -
47A GLN* 4.3 2.6 - - - +
48A HIS* 3.3 53.5 + - - +
49A GLU 5.6 0.2 + - - -
50A ASP* 5.7 5.1 - - - +
51A TYR* 5.0 10.3 - - - +
66A LYS* 4.3 3.8 - - - +
90A ASN 2.7 20.5 + - - -
91A SER* 3.7 14.7 + - - +
92A VAL 3.4 3.6 + - - +
93A HIS* 1.3 75.6 - - - +
95A GLY* 1.3 55.3 + - - +
96A HIS* 2.9 24.9 + - + +
295A LYS* 4.3 5.3 + - - -
409A ASN* 5.2 0.2 + - - -
615A MET* 3.6 65.5 + - + +
616A THR* 4.0 22.1 - - - +
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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