Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 4CY1
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 VAL 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A SER* 4.1 5.4 + - - -
105A ALA* 3.4 38.5 - - + +
106A SER 3.0 15.9 + - - +
107A ASP* 5.0 0.2 - - - +
109A LYS 3.5 33.0 - - - +
110A THR 3.7 9.6 - - - +
111A LEU* 3.7 22.2 - - + -
128A HIS* 3.6 25.1 - - + -
131A TYR* 1.3 75.6 - - - +
133A PHE* 1.3 61.2 + - - +
134A CYS 4.1 0.9 - - - +
146A SER* 4.1 4.3 - - - -
147A GLY 3.5 12.1 - - - +
148A SER* 4.3 0.7 - - - +
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Residues in contact with PHE 133 (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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91A SER* 3.5 9.4 - - - -
92A ASP* 3.4 8.1 - - - +
105A ALA* 4.1 3.8 - - - -
131A TYR 3.7 0.4 + - - -
132A VAL* 1.3 73.7 - - - +
134A CYS* 1.3 59.2 + - - +
147A GLY 2.9 8.8 + - - +
148A SER* 4.8 1.1 - - - -
149A PHE* 3.7 32.1 - + + -
174A VAL 3.8 13.9 - - - +
175A SER* 3.3 35.0 - - - -
191A TYR* 4.1 5.8 - - - -
261A CYS* 3.6 33.7 - - + -
591D ALA* 3.7 17.0 - - + -
592D ARG* 3.0 69.8 + - + -
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Residues in contact with CYS 134 (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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92A ASP* 3.3 12.1 - - - +
105A ALA* 4.0 1.5 - - - +
132A VAL* 3.8 2.8 - - - +
133A PHE* 1.3 78.1 - - - +
135A CYS* 1.3 67.1 + - - +
146A SER* 3.3 4.2 - - - -
147A GLY* 3.1 46.7 + - - +
174A VAL 3.5 9.4 - - - -
175A SER 3.7 11.9 - - - +
176A ALA* 3.5 39.3 - - + -
177A VAL* 3.7 6.1 - - - +
592D ARG* 4.0 2.9 - - - +
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Residues in contact with CYS 135 (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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52A LYS* 4.5 0.9 + - - -
92A ASP* 3.0 28.8 + - - +
93A VAL* 4.3 2.2 - - - -
94A ALA* 3.6 8.9 - - - +
103A VAL* 3.6 34.1 - - + -
104A SER 4.0 1.1 - - - -
105A ALA* 3.9 22.0 - - - -
111A LEU* 3.6 20.2 - - + -
134A CYS* 1.3 78.6 - - - +
136A ASN* 1.3 76.4 + - - +
144A ILE* 4.8 0.2 - - + -
145A VAL 3.2 10.1 - - - +
177A VAL* 4.1 3.5 + - - +
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Residues in contact with ASN 136 (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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52A LYS* 4.4 9.1 + - - +
92A ASP* 5.5 0.4 + - - -
94A ALA* 3.7 16.6 - - - +
95A TRP 5.6 0.5 - - - +
103A VAL* 4.5 1.1 - - - +
135A CYS* 1.3 80.5 + - - +
137A PHE* 1.3 69.5 + - - +
144A ILE* 3.3 6.3 - - - -
145A VAL* 2.8 42.2 + - + +
177A VAL 2.9 26.8 + - - +
178A HIS* 3.5 29.1 - - + +
179A PHE* 4.8 0.9 - - + +
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Residues in contact with PHE 137 (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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94A ALA* 3.5 21.7 - - - +
95A TRP 3.4 25.3 + - - +
96A SER* 3.6 15.5 - - - -
97A SER 5.2 0.2 - - - +
101A LEU* 4.0 21.5 - - + -
102A LEU 3.9 4.0 - - - -
103A VAL* 3.5 20.6 - - + -
113A ILE* 4.6 2.5 - - + -
136A ASN* 1.3 82.5 + - - +
138A ASN* 1.3 68.9 + - - +
139A PRO* 4.7 0.3 - - - +
141A SER* 3.8 21.8 - - - +
143A LEU 3.4 11.7 - - - -
144A ILE* 3.7 31.2 - - + +
158A VAL* 3.7 18.2 - - + -
179A PHE* 3.4 11.5 + - - +
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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