Contacts of the strand formed by residues 98 - 106 (chain B) in PDB entry 2W8B
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 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 4.6 0.4 - - - +
36B PRO 5.2 0.8 + - - -
37B ILE* 3.4 10.4 - - + +
38B GLY 3.0 22.5 + - - -
96B ILE* 3.1 5.4 - - - +
97B ASP* 1.3 89.2 + - - +
99B VAL* 1.3 63.1 + - - +
118B LEU* 3.8 22.0 - - + -
119B VAL 3.3 10.3 - - - +
121B THR* 3.2 2.3 + - - -
129B LEU* 4.6 5.6 - - + -
156B LEU* 4.4 21.1 - - + -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.2 9.2 - - - +
40B VAL* 3.8 18.6 - - + -
80B PRO* 4.9 0.2 - - + -
86B VAL* 4.6 10.1 - - + -
91B TRP* 3.4 48.7 - - + -
98B ALA* 1.3 80.7 - - - +
100B VAL* 1.3 76.5 + - - +
101B VAL* 4.0 9.2 - - + -
117B GLN 3.6 2.1 - - - +
118B LEU* 3.6 2.7 - - - -
119B VAL* 2.8 37.2 + - + +
121B THR* 3.6 16.6 - - + +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.7 5.2 - - + -
38B GLY 2.8 17.2 + - - +
39B VAL* 4.1 18.6 - - + -
40B VAL* 2.8 35.4 + - - +
42B PHE* 4.1 21.1 - - + -
58B VAL* 4.5 14.4 - - + -
62B LEU* 5.0 0.2 - - + -
99B VAL* 1.3 72.9 - - - +
101B VAL* 1.3 72.9 + - - +
116B TYR* 4.3 12.8 - - + -
117B GLN 3.5 5.8 - - - +
118B LEU* 4.1 17.5 - - + -
148B ALA* 6.3 0.2 - - + -
152B VAL* 4.2 20.9 - - + -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.3 5.8 - - + -
42B PHE* 3.9 6.1 - - - -
80B PRO* 3.6 28.9 - - + +
82B SER* 3.9 23.8 - - - +
83B ALA 4.0 2.2 - - - +
86B VAL* 3.8 23.8 - - + -
99B VAL* 4.0 6.3 - - + +
100B VAL* 1.3 80.1 - - - +
102B GLY* 1.3 59.1 + - - +
116B TYR* 3.3 6.8 - - - +
117B GLN* 2.8 58.7 + - + +
119B VAL* 4.2 7.6 - - + -
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Residues in contact with GLY 102 (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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41B PRO 4.7 0.8 + - - +
42B PHE* 3.2 22.5 - - - +
43B GLN* 2.7 29.8 + - - +
80B PRO 5.4 0.2 + - - -
81B GLY* 4.2 2.4 + - - +
101B VAL* 1.3 79.4 - - - +
103B GLN* 1.3 71.9 + - - +
115B ALA 3.1 14.1 - - - -
116B TYR* 3.9 0.9 - - - -
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Residues in contact with GLN 103 (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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42B PHE* 3.6 0.8 - - - -
43B GLN* 3.4 18.2 - - + +
81B GLY 3.0 26.3 + - - +
82B SER* 4.2 3.0 - - - +
102B GLY* 1.3 88.0 - - - +
104B VAL* 1.3 68.3 + - - +
105B THR* 4.8 10.3 - - + -
113B ASN 3.7 1.9 - - - +
115B ALA* 2.9 41.9 + - + +
117B GLN* 2.9 42.4 + - - -
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Residues in contact with VAL 104 (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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42B PHE* 4.2 13.7 - - + -
43B GLN 2.7 10.7 + - - +
44B TRP* 3.4 25.1 - - + -
45B ALA 3.2 23.2 + - - -
50B ALA* 5.2 4.3 - - + -
51B PRO* 4.5 10.1 - - + -
52B GLU 5.2 4.9 - - - +
54B ILE* 3.7 30.7 - - + +
103B GLN* 1.3 77.7 - - - +
105B THR* 1.3 69.0 + - - +
112B TYR* 4.2 17.5 - - + -
113B ASN 3.2 7.9 - - - +
114B VAL* 4.2 9.6 - - + -
141B LEU* 5.0 2.0 - - + -
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Residues in contact with THR 105 (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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44B TRP* 4.3 0.2 - - - -
45B ALA* 3.6 17.7 - - + -
103B GLN* 4.8 10.5 - - + -
104B VAL* 1.3 83.4 - - - +
106B PRO* 1.3 72.8 - - - +
112B TYR* 3.2 9.2 - - - -
113B ASN* 2.8 55.9 + - - +
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Residues in contact with PRO 106 (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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44B TRP* 3.9 19.0 - - + -
45B ALA* 3.4 28.9 - - + +
46B GLY* 5.4 0.4 - - - -
105B THR* 1.3 94.0 - - - +
107B ASN* 1.3 65.8 + - - +
108B PRO* 4.8 1.0 - - - +
111B SER 3.7 5.8 - - - +
112B TYR* 4.0 9.0 - - + -
113B ASN* 4.4 1.0 + - - -
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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