Contacts of the strand formed by residues 98 - 106 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 4.6 0.4 - - - +
36A PRO 5.2 0.6 + - - -
37A ILE* 3.4 9.5 - - + +
38A GLY 3.0 22.3 + - - -
96A ILE* 3.2 6.1 - - - +
97A ASP* 1.3 91.4 + - - +
99A VAL* 1.3 63.9 + - - +
118A LEU* 3.8 20.4 - - + -
119A VAL 3.4 9.2 - - - +
121A THR* 3.1 2.3 + - - -
129A LEU* 5.0 2.7 - - + -
156A LEU* 4.0 24.5 - - + -
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Residues in contact with VAL 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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38A GLY* 3.2 7.2 - - - +
40A VAL* 3.7 28.0 - - + -
80A PRO* 4.9 0.4 - - + -
86A VAL* 4.7 8.7 - - + -
91A TRP* 3.4 43.1 - - + +
98A ALA* 1.3 81.4 - - - +
100A VAL* 1.3 69.8 + - - +
101A VAL* 4.1 8.7 - - + -
117A GLN 3.7 1.0 - - - +
118A LEU* 3.6 3.2 - - - -
119A VAL* 2.9 37.0 + - + +
121A THR* 3.6 22.4 - - + +
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Residues in contact with VAL 100 (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 ILE* 4.3 10.1 - - + -
38A GLY 2.7 16.7 + - - +
39A VAL* 4.1 14.6 - - + -
40A VAL* 2.9 31.4 + - - +
42A PHE* 4.1 19.7 - - + -
58A VAL* 4.3 15.5 - - + -
99A VAL* 1.3 72.9 - - - +
101A VAL* 1.3 72.8 + - - +
116A TYR* 4.4 7.9 - - + -
117A GLN 3.6 5.4 - - - +
118A LEU* 4.1 9.2 - - + -
148A ALA* 6.2 0.2 - - + -
152A VAL* 4.1 33.7 - - + -
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Residues in contact with VAL 101 (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 VAL* 3.9 12.1 - - + -
42A PHE* 3.9 7.4 - - - -
80A PRO* 3.3 46.7 - - + +
82A SER* 3.9 20.4 - - - +
83A ALA* 4.1 4.9 - - - +
86A VAL* 4.2 4.0 - - + -
99A VAL* 4.1 7.2 - - + -
100A VAL* 1.3 80.2 - - - +
102A GLY* 1.3 60.3 + - - +
116A TYR* 3.2 8.1 - - - +
117A GLN* 2.9 50.7 + - + +
119A VAL* 4.5 4.9 - - + -
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Residues in contact with GLY 102 (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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41A PRO 4.8 0.6 + - - +
42A PHE* 3.4 20.7 - - - +
43A GLN* 3.0 20.6 + - - +
80A PRO 5.3 0.4 + - - -
81A GLY* 3.8 3.3 - - - +
101A VAL* 1.3 80.6 - - - +
103A GLN* 1.3 78.2 + - - +
115A ALA 3.0 14.1 - - - -
116A TYR* 3.9 1.1 - - - -
117A GLN* 4.4 0.2 - - - -
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Residues in contact with GLN 103 (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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42A PHE* 3.5 1.7 - - - -
43A GLN* 3.5 24.0 - - + +
81A GLY 2.8 28.1 + - - +
82A SER* 4.0 4.4 - - - +
102A GLY* 1.3 84.6 - - - +
104A VAL* 1.3 65.6 + - - +
105A THR* 4.2 13.5 - - + -
113A ASN 3.8 0.7 - - - +
114A VAL* 3.7 0.5 - - - -
115A ALA* 2.9 42.5 + - + +
117A GLN* 3.1 40.8 + - - -
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Residues in contact with VAL 104 (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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42A PHE* 4.4 13.0 - - + -
43A GLN 2.9 9.8 + - - +
44A TRP* 3.1 32.9 - - + -
45A ALA 3.2 12.3 + - - -
50A ALA* 4.8 10.8 - - + -
51A PRO* 4.7 9.4 - - + -
52A GLU 5.1 1.1 - - - +
54A ILE* 3.8 29.8 - - + -
103A GLN* 1.3 78.7 - - - +
105A THR* 1.3 67.0 + - - +
112A TYR* 4.2 15.5 - - + -
113A ASN 3.3 9.9 - - - +
114A VAL* 4.3 11.9 - - + -
141A LEU* 5.0 2.9 - - + -
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Residues in contact with THR 105 (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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44A TRP* 4.2 3.6 - - - -
45A ALA* 3.6 16.8 - - + -
103A GLN* 4.6 11.2 - - + -
104A VAL* 1.3 84.5 - - - +
106A PRO* 1.3 71.8 - - - +
112A TYR* 3.4 5.4 - - - -
113A ASN* 2.9 55.7 + - - +
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Residues in contact with PRO 106 (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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44A TRP* 3.9 11.0 - - + -
45A ALA* 3.3 28.9 - - + +
46A GLY* 5.7 0.4 - - - -
105A THR* 1.3 90.2 - - - +
107A ASN* 1.3 67.2 + - - +
108A PRO* 4.5 1.9 - - - +
111A SER 3.8 5.8 - - - +
112A TYR* 3.9 17.5 - - + -
113A ASN* 4.4 1.2 + - - -
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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