Contacts of the strand formed by residues 119 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ARG* 3.9 16.8 - - - +
118A ARG* 1.3 80.6 - - + +
120A VAL* 1.3 62.3 + - - +
121A ARG 4.1 0.9 + - - -
366A HIS* 4.9 15.5 + - + +
367A ILE 3.6 6.5 - - - +
368A GLU* 4.0 15.9 - - + +
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Residues in contact with VAL 120 (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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117A ARG* 4.6 6.3 - - + +
119A ARG* 1.3 75.8 - - - +
121A ARG* 1.3 62.1 + - - +
122A LEU* 3.8 7.6 - - + +
328A ALA* 3.8 36.8 - - + +
331A CYS* 4.0 14.8 - - + -
332A ALA* 4.4 12.1 - - + +
337A PHE* 4.2 16.2 - - + -
340A LEU* 4.9 2.0 - - + -
366A HIS* 3.2 5.4 - - - -
367A ILE* 2.8 60.5 + - + +
369A LEU* 4.8 4.5 - - + -
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Residues in contact with ARG 121 (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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119A ARG 4.1 1.8 + - - -
120A VAL* 1.3 75.4 - - - +
122A LEU* 1.3 71.1 + - - +
164A ASP* 3.0 37.4 + - - +
165A ALA* 4.1 9.0 - - - +
210A GLU* 3.6 33.3 + - - +
237A LEU* 6.3 0.2 - - - +
337A PHE* 3.5 12.6 - - + -
338A ALA* 3.9 12.1 + - - +
339A VAL* 3.1 27.4 - - + +
340A LEU 3.1 19.4 + - - -
365A GLY 4.6 2.0 - - - +
366A HIS* 3.0 32.0 + - + +
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Residues in contact with LEU 122 (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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120A VAL* 3.8 9.2 - - + +
121A ARG* 1.3 95.8 - - - +
123A TYR* 1.3 64.4 + - - +
163A PHE* 3.5 28.0 - - + -
164A ASP* 4.4 3.8 - - - +
165A ALA* 3.8 9.7 - - - +
324A THR* 5.7 0.9 - - + -
339A VAL* 4.4 4.1 - - - +
340A LEU* 3.1 33.2 - - + +
341A GLU 5.5 0.9 - - - +
342A TRP* 4.4 9.4 - - + -
362A ILE* 3.5 39.3 - - + -
365A GLY 3.2 11.8 + - - +
366A HIS* 4.2 0.7 - - - +
367A ILE* 3.8 30.3 - - + -
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LEU* 1.3 76.0 - - - +
124A ALA* 1.3 61.7 + - - +
125A ASP* 4.0 1.8 - - - -
163A PHE* 4.1 4.7 - - - -
165A ALA* 3.1 31.4 - - + +
166A ILE 4.4 0.9 - - - +
167A LYS* 3.6 47.3 + - + +
212A ALA* 6.2 0.4 - - + -
237A LEU* 5.6 2.7 - - + -
238A TRP* 3.9 23.5 - + - -
287A MSE 4.4 4.9 - - - +
314A ALA* 5.2 1.4 + - + -
315A PRO 4.7 4.1 + - - -
339A VAL* 3.2 33.0 - - + -
340A LEU 3.1 9.6 + - - -
341A GLU* 3.3 49.1 + - + +
342A TRP* 2.9 21.3 + - - +
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Residues in contact with ALA 124 (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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123A TYR* 1.3 74.8 - - - +
125A ASP* 1.3 67.9 + - - +
126A CYS* 3.8 3.5 - - - -
158A ALA* 4.4 16.2 - - + -
163A PHE* 4.1 18.7 - - + -
165A ALA 3.0 8.7 + - - +
166A ILE* 3.2 5.0 - - - -
167A LYS 2.9 24.0 + - - -
342A TRP* 3.3 27.8 - - + +
345A ILE* 4.8 4.7 - - + -
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Residues in contact with ASP 125 (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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123A TYR* 4.0 1.4 - - - -
124A ALA* 1.3 77.8 - - - +
126A CYS* 1.3 63.8 + - - +
127A ASN* 4.2 4.4 + - + +
167A LYS* 3.1 38.6 + - - +
341A GLU* 2.7 28.5 - - - +
342A TRP 3.0 11.5 + - - +
343A HIS* 3.1 39.4 - - + +
345A ILE* 3.6 22.3 + - - +
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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