Contacts of the strand formed by residues 84 - 91 (chain B) in PDB entry 2I6A
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 ALA 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.4 20.9 - - + -
70B ILE* 3.7 33.0 - - + +
74B GLN* 3.0 18.2 + - + +
77B ILE* 5.3 1.3 - - + -
82B LYS 4.1 1.3 - - - -
83B ALA* 1.3 79.8 - - + +
85B THR* 1.3 61.3 + - - +
108B VAL* 3.6 5.6 - - + +
109B ASP* 3.0 26.7 + - - +
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Residues in contact with THR 85 (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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7B ASN* 2.6 36.8 + - - +
9B LEU 2.8 15.3 + - - -
10B PHE* 3.8 18.8 - - + -
11B GLY* 3.2 20.1 + - - -
70B ILE* 3.7 9.8 - - - +
84B ALA* 1.3 72.6 - - - +
86B PHE* 1.3 67.1 + - - +
87B PHE* 3.8 26.2 - - + -
108B VAL* 4.5 0.2 - - - -
109B ASP 3.5 13.5 - - - +
158B LEU* 4.3 16.1 + - + +
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Residues in contact with PHE 86 (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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11B GLY 3.2 15.5 - - - -
13B GLY 3.6 33.2 - - - -
14B ASN 4.6 0.4 - - - -
15B PRO* 4.2 9.0 - - + -
66B THR* 3.8 10.1 - - + -
67B GLN* 3.4 64.2 - - + -
70B ILE* 4.2 6.1 - - + -
85B THR* 1.3 81.1 - - - +
87B PHE* 1.3 75.0 + - - +
108B VAL* 4.0 19.3 - - + -
109B ASP 3.2 5.5 + - - -
110B ALA* 3.4 4.4 - - + +
111B HIS 2.9 27.2 + - - +
112B TYR* 3.8 21.3 - + - -
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Residues in contact with PHE 87 (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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10B PHE* 3.6 27.6 - + - -
11B GLY 3.1 7.5 + - - -
12B MET* 3.3 14.1 - - + +
13B GLY 3.2 26.0 + - - +
85B THR* 3.8 15.7 - - + -
86B PHE* 1.3 87.3 - - - +
88B GLY* 1.3 58.7 + - - +
111B HIS* 3.4 36.1 - + + -
144B TYR* 3.8 16.6 - - + +
149B HIS* 3.4 16.2 - + + -
150B LEU* 4.1 7.4 - - + -
155B ASN* 3.5 45.1 - - + -
158B LEU* 4.2 7.6 - - + -
159B VAL* 3.8 9.0 - - + -
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Residues in contact with GLY 88 (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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13B GLY 3.7 13.5 - - - -
15B PRO* 3.8 10.1 - - - -
87B PHE* 1.3 77.4 - - - +
89B CYS* 1.3 56.6 + - - -
111B HIS 3.7 4.6 + - - -
112B TYR* 3.0 13.1 - - - +
113B TYR 2.7 29.8 + - - -
144B TYR* 4.1 15.9 - - - -
171B PHE* 5.6 0.7 - - - -
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Residues in contact with CYS 89 (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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13B GLY 4.8 0.2 + - - -
15B PRO* 3.0 21.8 - - - +
88B GLY* 1.3 74.1 - - - -
90B ILE* 1.3 65.5 + - - +
113B TYR* 3.4 35.7 - - + +
115B GLN* 3.8 8.3 - - - -
140B ALA 3.1 25.3 - - - +
141B ALA* 3.7 16.6 + - - +
143B CYS* 3.3 32.3 - - - -
144B TYR* 4.1 11.7 - - + +
171B PHE* 6.0 0.2 - - - -
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Residues in contact with ILE 90 (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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15B PRO* 3.6 25.8 - - + +
89B CYS* 1.3 81.3 - - - +
91B GLY* 1.3 56.3 + - - +
96B GLY* 4.3 9.2 - - - -
99B LEU* 4.1 17.7 - - + -
100B LYS* 3.4 39.9 - - + -
112B TYR* 3.6 28.7 - - + -
113B TYR 3.0 10.1 + - - +
114B GLU* 3.7 16.4 - - + +
115B GLN* 2.7 29.1 + - - +
120B THR* 3.8 8.5 - - + +
140B ALA* 3.6 7.1 - - - +
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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
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90B ILE* 1.3 80.6 - - - +
92B ILE* 1.3 62.7 + - - +
93B ASP* 3.1 11.1 + - - +
96B GLY* 3.9 9.0 - - - -
114B GLU* 5.0 2.4 - - - +
115B GLN* 3.3 13.2 - - - -
118B GLN 3.3 14.1 - - - -
119B PRO* 4.2 0.4 - - - -
120B THR* 2.8 24.5 + - - -
140B ALA* 3.7 3.4 - - - +
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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
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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