Contacts of the strand formed by residues 112 - 118 (chain B) in PDB entry 4ZMV
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 THR 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLN* 2.9 20.9 + - - +
111B ASP* 1.3 85.3 + - - +
113B PHE* 1.3 61.9 + - - +
114B ARG* 3.5 37.9 + - - +
206B VAL* 3.6 21.9 - - + +
208B VAL* 4.1 12.8 - - + -
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Residues in contact with PHE 113 (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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108B PHE* 3.8 17.0 - + - -
109B THR* 3.7 18.6 - - - -
110B GLN* 3.3 54.3 - - + +
112B THR* 1.3 76.6 - - - +
114B ARG* 1.3 61.9 + - - +
128B MET* 3.6 17.2 - - + +
129B GLN 4.3 6.3 - - - -
130B VAL* 3.5 22.2 - - + -
131B THR* 3.7 29.2 - - - -
191B ILE* 4.1 3.6 - - + -
205B ALA* 4.6 1.1 - - + -
206B VAL 3.1 18.3 + - - +
207B ALA* 3.2 1.6 - - - -
208B VAL* 2.8 27.0 + - - +
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Residues in contact with ARG 114 (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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110B GLN* 5.0 1.4 - - - +
112B THR* 3.5 30.5 + - - +
113B PHE* 1.3 76.4 - - - +
115B GLY* 1.3 58.7 + - - +
128B MET* 3.4 12.2 - - - +
208B VAL* 3.4 27.8 - - + +
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Residues in contact with GLY 115 (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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114B ARG* 1.3 76.9 - - - +
116B SER* 1.3 63.4 + - - -
127B VAL 5.2 0.4 - - - -
128B MET* 3.5 21.6 - - - +
208B VAL 3.1 8.7 + - - +
209B VAL* 4.3 4.9 - - - -
210B GLU* 2.9 24.5 + - - +
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Residues in contact with SER 116 (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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115B GLY* 1.3 75.9 - - - -
117B VAL* 1.3 66.5 + - - +
127B VAL* 3.7 20.9 + - - +
209B VAL* 4.4 2.7 - - - -
210B GLU* 3.1 28.0 - - - +
212B LEU* 3.5 23.1 - - - +
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Residues in contact with VAL 117 (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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116B SER* 1.3 82.2 - - - +
118B LEU* 1.3 60.0 + - - +
121B VAL* 3.7 32.5 - - + -
125B THR* 5.1 0.9 - - + -
126B SER 4.9 7.6 - - - +
127B VAL* 4.1 23.3 - - + -
163B PHE* 4.6 0.9 - - + -
174B VAL* 4.3 2.7 - - + -
179B LEU* 4.4 12.1 - - + -
209B VAL* 4.2 10.5 - - + -
210B GLU 3.0 1.8 + - - -
211B ILE* 3.5 26.0 - - + -
212B LEU* 2.7 34.5 + - - +
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Residues in contact with LEU 118 (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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117B VAL* 1.3 77.9 - - - +
119B GLU* 1.3 65.1 + - + +
120B GLY* 3.0 7.4 + - - +
121B VAL* 3.1 35.8 + - + +
179B LEU* 4.8 0.9 - - - +
212B LEU* 3.5 24.7 - - + +
213B ASP* 3.8 24.0 - - - +
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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