Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 2O5F
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 ARG 35 (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* 6.2 0.2 - - - +
10B ASP* 4.2 17.1 + - + +
12B VAL* 3.9 20.3 - - + +
16B ASP* 2.7 53.2 + - - +
18B VAL* 3.8 22.4 - - - +
34B VAL* 1.3 77.2 - - - +
36B VAL* 1.3 68.4 + - - +
71B ALA* 3.5 3.6 - - - +
72B VAL* 2.8 39.5 + - + +
76B GLU 4.4 13.3 + - - -
77B THR* 5.9 0.6 - - - +
78B TYR* 2.8 38.5 - - + +
115B PHE* 3.4 6.7 - - + -
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Residues in contact with VAL 36 (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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31B TRP* 4.1 19.5 - - + -
34B VAL* 4.7 1.1 - - + -
35B ARG* 1.3 81.3 - - - +
37B VAL* 1.3 68.7 + - - +
38B ASN* 4.0 14.4 - - - +
70B GLY 3.4 11.9 - - - +
71B ALA* 3.8 13.0 - - - +
72B VAL* 3.9 2.0 - - - -
78B TYR* 3.7 3.1 - - - -
113B SER* 5.7 0.9 - - - +
114B SER* 4.0 23.3 - - - +
115B PHE 2.9 9.6 + - - +
116B MET* 3.1 45.6 - - + -
117B CYS 3.5 2.6 + - - -
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Residues in contact with VAL 37 (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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36B VAL* 1.3 80.5 - - - +
38B ASN* 1.3 66.6 + - - +
69B GLY* 3.2 3.7 - - - -
70B GLY 2.9 47.3 + - - +
71B ALA 5.4 0.2 - - - +
72B VAL* 3.8 13.5 - - + -
78B TYR* 3.4 35.4 - - + +
81B ALA* 3.9 25.6 - - + +
82B PHE* 4.1 6.7 - - + +
84B ARG* 5.9 0.2 - - - +
85B GLU* 4.8 6.3 - - + -
117B CYS 3.4 7.0 - - - +
119B TYR* 4.2 15.0 - - + -
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Residues in contact with ASN 38 (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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36B VAL* 4.0 8.1 - - - +
37B VAL* 1.3 82.4 - - - +
39B ALA* 1.3 62.5 + - - +
66B VAL* 3.4 29.6 - - + +
68B VAL 3.4 4.9 - - - -
69B GLY* 3.9 2.9 - - - -
70B GLY 4.9 0.3 + - - -
82B PHE* 5.7 0.2 - - - -
116B MET* 3.4 35.0 - - - +
117B CYS 3.2 5.0 + - - +
118B VAL* 3.0 19.9 - - + -
119B TYR* 2.8 23.7 + - - -
156B LYS* 4.6 7.6 + - - -
158B ASP* 5.5 1.4 + - - +
162B LEU* 3.8 18.0 - - + +
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Residues in contact with ALA 39 (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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38B ASN* 1.3 77.7 - - - +
40B PHE* 1.3 65.7 + - - +
66B VAL* 3.9 3.7 - - - +
67B SER* 3.2 8.1 + - - -
68B VAL* 2.7 54.2 + - + -
82B PHE* 3.4 26.0 - - + -
118B VAL* 4.6 0.7 - - - -
119B TYR* 3.1 15.7 - - + +
120B GLU* 5.3 0.2 - - - -
121B LEU* 5.5 2.7 - - + +
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Residues in contact with PHE 40 (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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39B ALA* 1.3 77.8 - - - +
41B LEU* 1.3 62.1 + - - +
42B ARG 3.7 0.9 + - - -
48B LEU* 3.9 20.4 - - + -
50B ILE* 4.6 7.0 - - + -
66B VAL* 4.0 30.1 - - + -
67B SER* 3.5 9.9 - - - -
102B LEU* 4.4 2.9 - - + -
118B VAL* 4.2 24.5 - - + -
119B TYR 2.9 7.9 + - - +
120B GLU* 3.3 5.0 - - - +
121B LEU* 2.8 26.9 + - - +
159B LEU* 4.2 7.4 - - + -
162B LEU* 4.1 21.8 - - + -
163B VAL* 3.7 30.3 - - + -
166B CYS* 4.7 1.3 - - + -
167B TYR* 3.3 38.6 - + - +
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Residues in contact with LEU 41 (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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40B PHE* 1.3 72.1 - - - +
42B ARG* 1.3 62.0 + - - +
47B GLN 3.7 0.2 - - - +
48B LEU* 3.1 5.1 - - - -
49B TRP* 2.9 36.7 + - + -
67B SER* 2.9 20.5 + - - +
90B LEU* 4.5 11.0 - - + -
92B VAL* 6.4 1.3 - - + -
121B LEU* 3.2 27.6 - - + +
123B SER* 3.5 24.7 - - - +
125B ALA 4.5 2.5 - - - +
127B PRO* 3.2 39.0 - - + -
139B TRP* 3.3 24.9 - - + -
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Residues in contact with ARG 42 (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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40B PHE 3.7 0.6 + - - -
41B LEU* 1.3 75.2 - - - +
43B ASN* 1.3 69.4 + - - +
46B GLY* 4.0 20.6 - - - -
47B GLN 3.2 11.0 - - - +
48B LEU* 3.6 19.1 - - + -
100B ARG* 4.6 4.8 - - - +
120B GLU* 3.1 41.2 + - + +
121B LEU 2.8 8.9 + - - +
122B ARG* 3.0 54.1 + - - +
123B SER 3.3 17.2 + - - -
167B TYR* 3.9 16.2 - - - -
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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