Contacts of the strand formed by residues 131 - 137 (chain B) in PDB entry 4QKB
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 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ALA* 3.8 18.9 + - + +
97B PHE* 3.6 27.9 - - + -
101B GLN* 3.1 24.0 + - - -
128B CYS* 4.3 1.6 - - - -
129B GLY 3.4 1.2 - - - -
130B ALA* 1.3 82.4 + - - +
132B ILE* 1.3 76.8 + - - +
166B ILE* 4.0 15.3 - - + -
167B LEU 3.6 2.7 - - - +
168B ARG* 4.3 10.0 + - + +
203B ARG* 3.6 4.2 - - - +
204B SER* 3.1 29.3 + - - -
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Residues in contact with ILE 132 (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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123B ASP* 3.3 31.6 - - + +
128B CYS* 4.0 15.0 - - - -
131B THR* 1.3 81.7 - - - +
133B ALA* 1.3 65.0 + - - +
165B TYR* 4.6 15.7 - - + +
166B ILE* 3.5 2.9 - - - -
167B LEU* 2.9 43.1 + - + +
172B ARG* 3.9 24.7 - - + +
177B HIS* 3.7 21.3 - - + +
201B ILE* 3.6 26.5 - - + -
202B CYS 3.5 3.8 - - - +
203B ARG* 4.3 2.0 - - + +
302B AKG 6.4 1.1 - - + -
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Residues in contact with ALA 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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92B VAL* 4.1 11.6 - - + +
96B ALA* 3.6 30.5 - - + -
97B PHE* 3.7 15.5 - - + -
132B ILE* 1.3 76.9 - - - +
134B GLY* 1.3 57.1 + - - +
135B LEU 4.3 0.2 + - - -
164B LEU* 4.3 5.7 - - + +
165B TYR 3.3 9.9 - - - +
166B ILE* 4.6 0.9 - - + -
200B VAL 3.6 2.1 - - - +
201B ILE* 3.5 2.2 - - - -
202B CYS* 2.9 39.1 + - + +
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Residues in contact with GLY 134 (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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133B ALA* 1.3 74.2 - - - +
135B LEU* 1.3 62.2 + - - -
136B SER 4.0 0.3 + - - -
163B SER 3.7 1.0 - - - +
164B LEU* 3.5 5.2 - - - +
165B TYR* 2.8 72.8 + - - -
199B SER* 6.0 0.2 - - - -
200B VAL 3.6 6.3 - - - -
201B ILE* 4.5 4.0 - - - -
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Residues in contact with LEU 135 (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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39B PHE* 3.8 20.4 - - + -
40B LEU* 3.8 29.2 - - + -
48B LEU* 4.2 19.5 - - + -
88B ILE* 4.4 9.0 - - + -
89B MSE 4.4 9.2 - - + -
92B VAL* 3.7 20.2 - - + -
133B ALA 5.9 0.2 - - - +
134B GLY* 1.3 72.2 - - - -
136B SER* 1.3 60.9 + - - +
137B LEU* 5.0 2.7 - - + -
163B SER 3.3 16.6 - - - +
164B LEU* 3.9 15.3 - - + -
198B ILE 4.1 0.2 - - - +
199B SER* 3.2 8.7 - - - -
200B VAL* 2.9 50.9 + - + +
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Residues in contact with SER 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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40B LEU* 4.9 0.2 - - - +
135B LEU* 1.3 71.8 - - - +
137B LEU* 1.3 66.4 + - - +
139B SER 5.0 2.0 - - - -
159B LEU* 3.9 18.0 - - - +
160B GLU 3.8 19.7 - - - -
161B PRO* 4.2 1.6 - - - -
162B GLY* 2.8 28.2 + - - -
163B SER* 3.2 12.6 + - - -
165B TYR* 4.7 2.9 - - - -
197B ARG* 2.9 35.7 + - - +
198B ILE 3.8 3.6 - - - -
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Residues in contact with LEU 137 (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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40B LEU* 3.8 26.5 - - + -
45B GLU* 4.6 18.2 - - + +
48B LEU* 3.7 35.9 - - + -
49B SER* 4.5 12.6 - - - +
52B LEU* 4.6 1.3 - - + -
135B LEU* 5.0 1.8 - - + -
136B SER* 1.3 88.5 - - - +
138B LEU* 1.3 71.5 + - + +
139B SER 3.0 12.0 + - - +
161B PRO* 4.5 4.3 - - - -
197B ARG* 3.8 6.8 - - - +
198B ILE* 2.8 52.6 + - + +
200B VAL* 4.6 8.1 - - + -
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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