Contacts of the strand formed by residues 100 - 106 (chain B) in PDB entry 4C58
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ARG* 3.9 17.3 - - + -
44B GLN 3.6 23.3 - - - +
45B ALA* 3.7 6.5 - - + +
46B PRO* 5.1 1.8 - - - -
98B ASP 3.2 3.7 + - - +
99B THR* 1.3 78.9 - - - +
101B ILE* 1.3 61.7 + - - +
102B TYR* 3.4 19.2 - - + -
123B GLN* 3.6 6.9 - - - +
124B VAL 3.0 29.7 + - - +
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Residues in contact with ILE 101 (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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43B ARG* 3.2 3.1 - - - +
44B GLN* 3.0 35.9 + - + +
100B ALA* 1.3 73.4 - - - +
102B TYR* 1.3 61.7 + - - +
103B TYR* 3.3 42.5 - - + +
120B GLN 4.9 0.7 - - - +
121B GLY* 3.8 19.1 - - - -
122B THR 3.5 9.6 - - - +
123B GLN* 3.4 25.6 - - + +
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Residues in contact with TYR 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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6B GLU* 3.8 1.7 - - - +
21B LEU* 3.8 30.1 - - + -
41B TRP* 4.2 5.6 - - + -
42B PHE 3.5 6.3 - - - -
43B ARG* 2.9 38.3 + - + -
53B VAL* 4.5 7.2 - - + -
76B PHE* 4.1 15.4 - + - -
89B LEU* 4.5 6.5 - - + -
91B MET* 4.0 18.1 - - - -
94B LEU* 5.0 0.2 - - - +
98B ASP* 2.6 37.3 + - - +
100B ALA* 3.4 19.7 - - + -
101B ILE* 1.3 74.3 - - - +
103B TYR* 1.3 60.9 + - - +
104B CYS 4.2 0.2 - - - -
121B GLY* 3.3 0.5 - - - -
122B THR* 2.8 44.4 + - + +
124B VAL* 3.7 21.0 - - + +
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Residues in contact with TYR 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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6B GLU* 3.6 3.8 - - - -
41B TRP* 3.3 4.7 - - - -
42B PHE* 2.8 79.4 + + + -
44B GLN* 4.4 16.6 + - + +
101B ILE* 3.3 48.7 - - + +
102B TYR* 1.3 72.9 - - - +
104B CYS* 1.3 66.0 + - - +
105B ALA 3.7 0.3 + - - -
118B ALA* 5.0 1.6 - - + -
119B GLY 3.5 20.2 - - - +
120B GLN 3.4 19.3 - - - -
121B GLY* 3.5 7.2 - - - -
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Residues in contact with CYS 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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4B LEU* 4.0 7.0 - - + -
6B GLU* 3.0 22.4 + - + +
23B CYS* 2.0 53.8 - - + -
39B MET* 3.7 19.5 - - - -
40B GLY 3.5 9.2 - - - -
41B TRP* 3.5 12.9 - - - +
103B TYR* 1.3 74.5 - - - +
105B ALA* 1.3 64.1 + - - +
118B ALA* 3.3 3.5 - - - +
119B GLY 2.8 25.1 + - - -
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Residues in contact with ALA 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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4B LEU* 4.0 3.6 - - - -
39B MET* 3.4 6.6 - - - +
40B GLY 2.8 32.8 + - - -
42B PHE* 4.0 14.6 - - + -
104B CYS* 1.3 80.0 - - - +
106B THR* 1.3 64.8 + - - +
107B THR* 5.4 0.2 - - - +
111B PHE* 3.9 18.6 - - + -
115B ALA* 3.8 20.6 - - + -
117B THR 3.2 13.0 - - - +
118B ALA* 4.3 0.2 - - - -
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Residues in contact with THR 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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2B VAL* 4.9 1.8 - - + +
4B LEU* 4.1 24.2 - - + -
29B THR* 3.5 33.0 - - + +
34B ARG 3.4 9.9 - - - +
39B MET* 4.2 7.9 - - + -
105B ALA* 1.3 78.9 - - - +
107B THR* 1.3 61.9 + - - +
115B ALA* 3.3 10.7 - - - +
116B ILE* 2.9 34.9 + - - +
117B THR* 2.9 32.8 + - + +
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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