Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 2C3V
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 ILE 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR 4.1 2.9 - - - +
88A ASP* 1.3 73.0 - - - +
90A THR* 1.3 61.1 + - - +
91A ILE* 4.1 7.6 - - + -
106A LEU* 3.8 29.2 - - + -
131A THR* 3.4 1.3 - - - -
132A ILE* 2.8 44.6 + - + +
134A ALA* 4.1 4.3 - - + -
138A SER* 4.0 13.9 - - - -
140A LEU* 3.9 24.5 - - + +
161A PHE* 3.8 36.3 - - + +
162A SER 3.6 21.8 - - - +
163A SER* 3.7 8.5 - - - +
164A GLY 3.5 3.4 - - - +
166A HIS* 4.6 0.4 - - + -
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Residues in contact with THR 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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88A ASP* 4.8 4.2 + - - +
89A ILE* 1.3 74.2 - - - +
91A ILE* 1.3 61.7 + - - +
92A TYR* 3.8 25.4 - - + +
129A LYS* 3.9 15.0 - - + -
130A VAL 3.4 5.4 - - - +
131A THR* 3.0 31.4 + - - +
164A GLY 2.9 7.4 + - - +
165A VAL* 3.3 21.8 - - + +
166A HIS* 3.0 30.1 + - - -
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 4.1 11.2 - - + -
90A THR* 1.3 79.2 - - - +
92A TYR* 1.3 74.8 + - - +
93A TYR* 4.7 1.8 - - + +
102A ILE* 3.7 23.6 - - + -
119A LEU* 4.5 1.7 - - + +
128A VAL 3.9 0.2 - - - +
129A LYS* 3.3 3.8 - - - +
130A VAL* 2.9 38.7 + - + +
132A ILE* 4.1 15.9 - - + -
140A LEU* 4.3 3.1 - - + -
144A PHE* 4.1 18.2 - - + -
161A PHE* 3.6 55.6 - - + -
166A HIS 3.4 3.6 - - - +
168A LEU* 5.2 0.4 - - + -
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Residues in contact with TYR 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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90A THR* 3.8 10.9 - - + +
91A ILE* 1.3 80.1 - - - +
93A TYR* 1.3 61.1 + - - +
94A LYS 4.3 0.2 - - - -
122A SER* 4.0 20.9 - - - -
124A TYI 4.0 12.9 - - + +
127A TYI 4.5 4.7 - - + -
128A VAL 3.2 7.0 - - - +
129A LYS* 3.5 45.8 + - + -
165A VAL* 3.7 24.8 - - + +
166A HIS 2.9 15.6 + - - -
167A THR* 3.4 19.7 - - + +
168A LEU* 2.9 26.6 + - - -
177A THR* 3.8 19.7 - - + +
178A PRO* 3.7 27.4 - - + -
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.7 1.3 - - + -
92A TYR* 1.3 75.3 - - - +
94A LYS* 1.3 74.0 + - - +
95A THR* 3.4 35.6 + - + -
97A TRP* 3.7 15.1 - + - -
100A PRO* 5.0 1.3 - - + -
119A LEU* 4.3 12.3 - - + -
127A TYI 3.3 4.5 - - - -
128A VAL* 2.8 51.3 + - + +
144A PHE* 3.7 36.6 - + + -
152A ASP* 2.6 41.6 + - - +
168A LEU* 3.4 33.4 - - + -
170A ASP 6.1 1.3 - - - -
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Residues in contact with LYS 94 (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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93A TYR* 1.3 84.8 - - - +
95A THR* 1.3 65.3 + - - +
126A GLY* 3.4 15.5 - - - +
127A TYI 3.3 30.5 - - + +
168A LEU 2.9 15.2 + - - +
169A ALA* 3.9 18.2 - - + -
170A ASP* 3.6 37.9 + - - +
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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