Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 2O8B
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PRO* 4.2 9.3 - - - +
32A THR* 3.0 23.2 + - - -
33A THR* 3.1 37.4 - - + +
34A VAL* 3.0 24.8 + - - +
93A LEU* 4.4 0.7 - - - -
98A TYR* 1.3 76.9 - - - +
100A VAL* 1.3 64.3 + - - +
101A GLU* 5.6 6.7 - - + -
122A LYS* 5.8 9.0 - - - +
123A ALA 3.3 14.8 - - - +
124A SER* 4.1 12.5 + - - -
125A PRO* 4.1 4.7 - - + -
198A GLU* 4.3 3.0 + - - -
223A LEU* 3.7 14.6 - - + +
224A ILE 3.2 18.6 + - - -
225A THR* 2.8 43.5 + - - +
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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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34A VAL 3.7 5.2 - - - +
36A LEU* 4.1 24.7 - - + -
89A VAL* 4.2 13.5 - - + -
92A LEU* 4.0 26.7 - - + -
93A LEU* 3.9 25.1 - - + -
99A ARG* 1.3 78.7 - - - +
101A GLU* 1.3 73.5 + - - +
102A VAL* 4.2 9.2 - - + -
122A LYS* 3.4 6.1 - - - +
123A ALA* 2.9 42.1 + - + +
131A PHE* 4.7 7.0 - - + -
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Residues in contact with GLU 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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33A THR* 5.5 13.5 - - - +
34A VAL 3.0 11.7 + - - +
35A ARG* 3.1 25.8 + - + -
36A LEU* 2.8 27.4 + - - +
99A ARG* 5.6 6.6 - - + -
100A VAL* 1.3 79.7 - - - +
102A VAL* 1.3 64.2 + - - +
103A TYR* 2.6 34.5 + - + -
119A LEU* 3.7 23.5 - - + +
121A TYR 3.6 2.9 - - - -
122A LYS* 4.8 16.0 - - + -
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Residues in contact with VAL 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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36A LEU* 3.4 10.8 - - + +
38A ASP* 4.6 7.9 - - + +
43A TYR* 4.4 19.3 - - + +
85A PHE* 3.7 31.2 - - + -
100A VAL* 4.2 12.6 - - + -
101A GLU* 1.3 77.6 - - - +
103A TYR* 1.3 65.0 + - - +
104A LYS* 5.3 0.7 - - + -
119A LEU* 3.7 2.5 - - - +
120A ALA* 2.8 32.6 + - + -
121A TYR* 3.0 39.5 + - + +
131A PHE* 4.3 9.9 - - + -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 6.0 0.9 - + - -
26A MET* 3.6 21.4 - - + +
27A PRO* 6.1 0.5 - - - +
35A ARG* 3.4 29.2 + - + -
36A LEU 2.9 15.9 + - - -
37A PHE* 3.6 31.8 - + + -
38A ASP 3.0 23.7 + - - -
101A GLU* 2.6 38.2 + - + -
102A VAL* 1.3 76.5 - - - +
104A LYS* 1.3 62.7 - - - +
117A TRP* 3.4 13.6 - - + -
118A TYR* 3.2 29.4 - - - +
119A LEU* 3.5 25.2 - - + +
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Residues in contact with LYS 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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38A ASP* 3.3 36.3 - - + +
102A VAL* 5.3 1.8 - - + -
103A TYR* 1.3 73.9 - - - +
105A ASN* 1.3 62.7 + - - +
117A TRP* 3.3 8.1 - - - -
118A TYR* 3.1 59.8 + - + +
120A ALA* 3.8 17.7 - - + +
121A TYR* 4.4 24.3 + - - -
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Residues in contact with ASN 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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38A ASP 4.6 4.2 + - - +
104A LYS* 1.3 77.0 - - - +
106A ARG* 1.3 67.5 + - - +
107A ALA* 2.8 26.4 + - + +
114A GLU 2.6 29.9 + - - +
115A ASN* 4.5 1.4 + - - -
116A ASP 3.0 19.9 + - - +
117A TRP* 3.6 39.8 - - + +
118A TYR* 4.3 4.9 + - - -
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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