Contacts of the strand formed by residues 132 - 137 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B SER* 4.1 5.7 + - - -
105B ALA* 3.5 38.3 - - + +
106B SER 3.0 16.4 + - - +
109B LYS* 3.5 33.2 - - - +
110B THR* 3.7 10.5 - - - +
111B LEU* 3.7 21.8 - - + -
128B HIS* 3.7 23.3 - - + -
131B TYR* 1.3 75.4 - - - +
133B PHE* 1.3 61.6 + - - +
134B CYS 4.2 0.7 - - - +
146B SER* 4.0 4.7 - - - -
147B GLY 3.5 12.3 - - - +
148B SER* 4.2 0.9 - - - -
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Residues in contact with PHE 133 (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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91B SER* 3.5 9.7 - - - -
92B ASP* 3.4 8.1 - - - +
105B ALA* 4.2 3.8 - - - -
131B TYR 3.8 0.4 + - - -
132B VAL* 1.3 73.0 - - - +
134B CYS* 1.3 60.4 + - - +
147B GLY 2.9 8.5 + - - +
148B SER* 4.7 0.9 - - - -
149B PHE* 3.6 32.1 - + + -
174B VAL 3.7 14.6 - - - +
175B SER* 3.3 34.3 - - - -
191B TYR* 4.2 5.2 - - - -
261B CYS* 3.6 31.6 - - + -
591C ALA* 3.7 17.3 - - + -
592C ARG* 2.9 72.6 + - + -
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Residues in contact with CYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ASP* 3.3 12.3 - - - +
105B ALA* 4.1 1.7 - - - +
132B VAL* 3.8 2.5 - - - +
133B PHE* 1.3 78.6 - - - +
135B CYS* 1.3 65.7 + - - +
146B SER* 3.3 4.7 - - - -
147B GLY* 3.0 46.8 + - - +
174B VAL 3.6 9.9 - - - -
175B SER 3.7 13.0 - - - +
176B ALA* 3.5 38.8 - - + -
177B VAL* 3.7 6.1 - - + +
592C ARG* 3.9 2.9 - - - +
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LYS* 4.4 1.2 + - - -
92B ASP* 3.0 37.3 + - - +
93B VAL* 4.1 3.1 - - - -
94B ALA* 3.6 5.9 - - - +
103B VAL* 3.7 33.2 - - + -
104B SER 4.1 0.9 - - - -
105B ALA* 3.9 13.7 - - + -
111B LEU* 3.5 22.4 - - + -
134B CYS* 1.3 77.4 - - - +
136B ASN* 1.3 74.9 + - - +
144B ILE* 4.7 0.4 - - + -
145B VAL 3.2 9.6 - - - +
177B VAL* 4.0 3.7 + - - +
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Residues in contact with ASN 136 (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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52B LYS* 4.3 10.2 + - - +
92B ASP* 5.6 0.4 + - - -
94B ALA* 3.6 16.7 - - - +
103B VAL* 4.6 0.6 - - - +
135B CYS* 1.3 82.2 + - - +
137B PHE* 1.3 69.8 + - - +
144B ILE* 3.3 5.5 - - - +
145B VAL* 2.8 42.9 + - + +
177B VAL 2.8 27.0 + - - +
178B HIS* 3.5 28.7 - - + -
179B PHE* 4.8 0.9 - - + -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA* 3.6 9.5 - - - +
95B TRP 3.4 24.1 + - - +
96B SER* 3.6 21.1 - - - -
101B LEU* 4.0 21.1 - - + -
102B LEU 4.0 4.7 - - - -
103B VAL* 3.5 30.1 - - + -
113B ILE* 4.7 2.2 - - + -
136B ASN* 1.3 82.7 + - - +
138B ASN* 1.3 69.5 + - - +
139B PRO* 4.6 0.2 - - - +
141B SER* 3.6 19.3 - - - +
143B LEU 3.4 11.0 - - - -
144B ILE* 3.7 21.1 - - + -
158B VAL* 3.7 30.1 - - + -
179B PHE* 3.4 11.9 - - - +
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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
------------------------------------------------------------
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