Contacts of the strand formed by residues 119 - 125 (chain B) in PDB entry 2QQ6
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 ARG 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ARG* 4.0 14.7 - - - +
118B ARG* 1.3 77.7 - - - +
120B VAL* 1.3 61.2 + - - +
121B ARG 4.2 0.7 + - - -
363B ARG 5.0 4.6 + - - -
364B GLU* 5.8 1.8 - - - +
366B HIS* 3.2 51.8 + - + +
367B ILE 3.1 10.8 - - - +
368B GLU* 2.9 40.5 + - - +
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Residues in contact with VAL 120 (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 ARG* 4.7 8.7 - - + +
118B ARG 4.9 2.5 - - - +
119B ARG* 1.3 77.3 - - - +
121B ARG* 1.3 66.7 + - - +
122B LEU* 3.8 2.7 + - + +
328B ALA* 3.8 45.1 - - + +
331B CYS* 4.0 7.2 - - + -
332B ALA* 4.6 7.9 - - + +
337B PHE* 4.0 17.7 - - + -
340B LEU* 4.4 14.4 - - + -
366B HIS* 3.2 5.7 - - - -
367B ILE* 2.8 45.4 + - + +
369B LEU* 5.4 2.5 - - + -
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Residues in contact with ARG 121 (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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119B ARG 4.2 1.0 + - - -
120B VAL* 1.3 74.6 - - - +
122B LEU* 1.3 67.6 + - - +
164B ASP* 3.4 47.0 + - - +
165B ALA* 4.0 8.1 - - - +
210B GLU* 2.8 29.9 + - - +
337B PHE* 3.4 13.0 - - + -
338B ALA 4.4 10.5 + - - +
339B VAL* 3.5 25.6 - - + +
340B LEU* 3.0 21.8 + - - +
365B GLY 4.0 2.9 - - - +
366B HIS* 3.2 31.9 + - + -
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Residues in contact with LEU 122 (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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120B VAL* 4.3 7.6 - - + +
121B ARG* 1.3 88.3 + - - +
123B TYR* 1.3 65.1 + - - +
163B PHE* 4.0 18.3 - - + -
164B ASP* 4.7 2.8 + - - +
165B ALA* 3.9 6.9 - - - +
324B THR* 5.1 2.7 - - + -
339B VAL* 3.7 4.7 - - - +
340B LEU* 3.0 45.3 - - + +
341B GLU 4.5 5.8 - - - +
342B TRP* 4.5 5.2 - - + -
362B ILE* 3.4 46.2 - - + -
365B GLY 2.8 17.7 + - - +
367B ILE* 3.8 21.8 - - + -
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Residues in contact with TYR 123 (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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122B LEU* 1.3 71.8 - - - +
124B ALA* 1.3 62.3 + - - +
125B ASP 4.8 1.1 - - - -
163B PHE* 4.1 4.3 - - - -
165B ALA* 3.3 28.7 - - + +
166B ILE 4.9 1.3 - - - -
167B LYS* 3.1 61.7 + - + -
212B ALA* 6.0 1.6 - - + -
237B LEU* 5.9 3.4 - - + -
238B TRP* 4.0 28.4 - + - -
240B GLU* 4.4 0.2 + - - -
287B MSE 5.0 2.3 - - - -
314B ALA 5.2 1.5 + - - -
315B PRO 4.5 5.0 + - - -
316B HIS* 4.9 2.4 - - - -
339B VAL* 4.0 23.3 - - + -
340B LEU 2.7 22.2 + - - -
341B GLU* 3.2 37.0 + - + +
342B TRP* 2.9 28.6 + - - +
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Residues in contact with ALA 124 (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 TYR* 1.3 72.4 - - - +
125B ASP* 1.3 65.2 + - - +
126B CYS* 3.4 4.4 + - - -
158B ALA* 4.1 19.7 - - + -
163B PHE* 3.8 29.0 - - + -
165B ALA 2.8 12.8 + - - +
166B ILE* 3.4 4.6 - - + -
167B LYS 2.8 24.3 + - - -
342B TRP* 3.8 12.6 - - + -
345B ILE* 4.9 6.5 - - + -
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Residues in contact with ASP 125 (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 TYR* 3.9 1.2 + - - -
124B ALA* 1.3 71.4 - - - +
126B CYS* 1.3 57.6 + - - +
127B ASN* 3.0 39.4 + - - +
128B ALA* 3.5 12.9 + - - +
167B LYS* 3.0 40.0 + - + +
168B LEU* 6.1 0.2 - - - -
169B ASP* 5.1 4.1 - - - +
341B GLU* 3.4 16.1 - - + +
342B TRP 3.1 19.0 + - - +
343B HIS* 3.6 23.2 + - + -
345B ILE* 4.1 17.3 - - - +
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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