Contacts of the strand formed by residues 98 - 104 (chain A) in PDB entry 2C0Q
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 TYR 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.5 19.5 - - - -
35A ILE 3.3 5.6 - - - +
36A PRO* 3.5 28.3 - - + -
37A PHE* 3.3 5.9 - - - -
40A PRO* 4.8 4.2 - - + +
66A GLN* 3.5 56.5 + - + -
67A ASN* 4.8 0.8 + - - -
95A ASP* 2.5 48.3 + - - -
96A CYS* 2.8 17.8 + - - +
97A LEU* 1.3 80.8 - - - +
99A LEU* 1.3 61.4 + - - +
100A ASN* 5.3 1.6 + - - +
150A ASN* 3.0 31.3 + - - +
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Residues in contact with LEU 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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34A GLY 3.1 5.5 + - - -
35A ILE* 2.8 64.7 + - + +
37A PHE* 3.8 22.9 - - + -
98A TYR* 1.3 74.6 - - - +
100A ASN* 1.3 68.7 + - - +
101A VAL* 4.2 6.3 - - + -
147A VAL* 4.6 8.1 - - + -
148A SER 3.3 13.7 - - - +
149A MET* 3.9 6.3 - - + -
179A ALA* 3.8 21.1 - - + +
182A TRP* 3.7 40.2 - - + -
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Residues in contact with ASN 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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32A PHE 3.3 4.3 - - - -
33A LEU* 3.6 15.7 - - + -
34A GLY* 3.0 26.3 + - - -
65A PHE* 3.5 29.3 - - - -
66A GLN 5.2 0.3 + - - -
98A TYR 5.3 1.0 + - - -
99A LEU* 1.3 77.5 + - - +
101A VAL* 1.3 64.1 + - - +
102A TRP* 4.1 7.6 - - + -
128A ALA* 3.4 20.4 - - - +
129A SER* 5.5 0.2 - - - -
146A LEU 3.8 0.6 - - - +
147A VAL* 3.2 9.0 - - - +
148A SER* 2.7 55.6 + - - +
150A ASN* 5.1 1.6 + - - -
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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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30A SER 3.8 0.7 - - - +
31A ALA* 3.3 5.7 - - - +
32A PHE* 2.7 49.5 + - + +
33A LEU* 4.7 0.2 - - - +
35A ILE* 3.9 18.2 - - + -
99A LEU* 4.2 2.2 - - + -
100A ASN* 1.3 79.4 - - - +
102A TRP* 1.3 64.1 + - - +
103A THR* 4.0 16.4 - - + -
145A VAL* 4.1 13.7 - - + -
146A LEU 3.4 3.4 - - - +
147A VAL* 4.2 9.2 - - + -
182A TRP* 4.1 22.4 - - + -
187A ILE* 4.2 3.8 - - + -
190A PHE* 3.9 25.4 - - + -
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Residues in contact with TRP 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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22A LEU* 4.0 10.1 - - + +
29A VAL* 4.2 5.4 - - + -
30A SER 3.3 6.5 - - - -
31A ALA* 3.7 22.0 - - + +
33A LEU* 3.8 11.9 - - + -
65A PHE* 3.8 36.8 - + - -
100A ASN* 4.1 8.1 - - + -
101A VAL* 1.3 75.6 - - - +
103A THR* 1.3 63.4 + - - +
128A ALA 4.7 2.2 - - - -
133A TYR 4.0 9.0 - - - -
134A ASP* 3.8 11.6 + - - -
135A GLY* 3.5 35.2 - - - +
136A ARG* 3.6 22.1 - - + +
139A ALA* 3.9 14.8 - - + -
144A ALA 3.8 0.7 - - - +
145A VAL* 3.3 5.9 - - - +
146A LEU* 2.8 55.7 + - + +
148A SER* 3.8 20.4 - - - -
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Residues in contact with THR 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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29A VAL* 3.7 4.5 - - - +
30A SER* 2.8 50.1 + - - +
32A PHE* 4.5 3.6 - - - -
101A VAL* 4.0 5.8 - - + -
102A TRP* 1.3 79.9 - - - +
104A PRO* 1.3 70.1 + - - +
107A ARG* 3.9 12.0 - - - +
108A PRO* 4.7 0.9 - - - -
139A ALA* 4.1 5.8 - - - -
144A ALA 4.0 1.3 - - - -
145A VAL* 3.4 29.2 - - + -
190A PHE* 3.6 28.7 - - + +
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Residues in contact with PRO 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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28A PRO 5.1 0.2 - - - +
29A VAL* 4.8 4.0 - - + -
30A SER* 3.6 7.8 - - - +
103A THR* 1.3 102.4 + - + +
105A TYR* 1.3 60.3 + - - +
106A PRO 3.5 13.0 - - - +
107A ARG* 3.5 11.1 + - - -
108A PRO* 4.0 20.4 - - + -
139A ALA* 3.7 22.2 - - - +
140A GLN* 5.6 1.1 - - - -
143A GLY* 3.8 21.1 - - - +
144A ALA 3.5 15.3 - - - +
145A VAL* 4.7 0.9 - - + -
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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