Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 1CCW
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 LEU 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP 3.6 12.0 + - - +
57A ALA* 3.4 8.0 - - + -
58A ILE 2.9 29.9 + - - -
85A GLY 3.5 4.9 + - - +
86A ILE* 1.4 77.6 - - - +
88A LEU* 1.3 59.4 - - - +
89A TYR* 4.1 9.0 - - + -
114A ASP* 3.3 20.4 - - + +
130A LEU* 3.7 25.4 - - + -
133A ASP* 4.0 31.2 - - + +
134A LEU* 3.8 25.1 - - + -
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Residues in contact with LEU 88 (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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58A ILE* 3.6 34.3 - - + +
60A VAL* 5.6 0.2 - - + -
74A LEU* 4.1 16.8 - - + -
75A ARG* 3.4 63.5 - - + +
78A CYS* 4.1 11.9 - - - -
86A ILE* 4.1 3.4 - - + +
87A LEU* 1.3 80.5 - - - +
89A TYR* 1.4 61.6 + - - +
112A GLY 3.8 7.9 - - - +
113A TYR* 3.7 18.0 - - + -
114A ASP* 2.8 36.7 + - - +
115A ARG 3.3 4.9 + - - -
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Residues in contact with TYR 89 (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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58A ILE 3.0 6.6 + - - +
59A LEU* 4.0 34.3 - - + -
60A VAL* 2.9 30.0 + - - +
87A LEU* 4.3 19.1 - - + -
88A LEU* 1.4 84.6 - - - +
90A VAL* 1.3 62.0 + - - +
113A TYR* 4.1 1.9 - - - -
114A ASP* 4.6 1.3 - - + -
115A ARG* 3.4 24.8 + - + +
117A TYR* 3.5 28.9 - + + -
126A GLY* 4.0 7.9 - - - -
129A ASP 3.3 3.6 + - - -
130A LEU* 3.2 45.1 + - + +
133A ASP* 2.6 30.5 + - - -
800A CNC 4.0 6.1 - - + -
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Residues in contact with VAL 90 (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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60A VAL* 3.2 15.3 - - + +
62A SER* 4.9 2.2 - - - -
71A CYS* 3.9 27.4 - - - -
89A TYR* 1.3 75.8 - - - +
91A GLY* 1.3 62.1 + - - +
94A ILE* 4.0 15.9 - - + -
108A PHE* 3.9 17.7 - - + -
113A TYR* 3.7 28.5 - - + -
115A ARG 3.0 13.0 + - - +
116A VAL* 3.4 14.8 - - + +
117A TYR* 2.8 27.2 + - - -
800A CNC 4.1 3.8 - - - -
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Residues in contact with GLY 91 (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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60A VAL 3.0 7.1 + - - -
61A SER* 3.4 4.0 - - - -
62A SER 2.9 25.5 + - - -
90A VAL* 1.3 77.2 - - - +
92A GLY* 1.3 56.5 + - - -
94A ILE* 3.4 11.0 - - - +
117A TYR* 3.6 20.0 - - - -
800A CNC 3.5 18.8 - - - -
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Residues in contact with GLY 92 (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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62A SER 3.6 2.7 - - - -
63A LEU* 3.7 5.8 - - - -
91A GLY* 1.3 72.1 - - - -
93A ASN* 1.3 63.3 + - - -
94A ILE* 3.8 2.8 + - - +
117A TYR* 4.0 3.3 + - - +
118A ALA 3.6 5.1 + - - +
119A PRO* 3.2 31.7 - - - +
800A CNC 3.5 32.7 + - - -
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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