Contacts of the strand formed by residues 122 - 127 (chain T) in PDB entry 2A2Q
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 LYS 122 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118T GLN* 2.8 11.4 - - - +
119T VAL 2.7 36.8 + - - +
121T THR* 1.3 98.6 - - + +
123T VAL* 1.3 59.2 + - - +
176T LEU* 3.7 38.4 - - + +
177T ILE 3.1 12.6 - - - +
178T ASP* 3.4 26.9 + - - +
179T VAL* 4.0 1.3 - - - -
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Residues in contact with VAL 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116T PHE* 4.1 8.1 - - + -
117T GLU 3.2 7.9 - - - +
118T GLN* 3.9 5.8 - - - +
122T LYS* 1.3 75.0 - - - +
124T ASN* 1.3 71.7 + - - +
125T VAL* 3.9 16.2 - - + -
175T PHE 3.4 2.4 - - - +
176T LEU* 3.5 3.7 - - - -
177T ILE* 2.9 37.7 + - + +
179T VAL* 3.4 37.7 - - + -
187T PHE* 4.0 14.4 - - + -
210T MET* 3.7 26.5 - - + -
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Residues in contact with ASN 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115T SER* 5.4 0.7 + - - -
116T PHE* 3.0 5.9 - - - +
117T GLU* 2.6 49.6 + - + +
119T VAL* 4.0 17.0 - - + +
122T LYS 4.2 0.2 - - - -
123T VAL* 1.3 73.8 - - - +
125T VAL* 1.3 58.5 + - - +
126T THR* 2.9 24.3 + - - -
174T GLU* 3.1 30.9 + - - +
175T PHE 3.1 17.1 + - - -
176T LEU* 4.2 13.4 - - + +
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Residues in contact with VAL 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T ILE* 4.0 23.3 - - + -
115T SER 3.6 10.3 - - - +
116T PHE* 4.2 7.0 - - + +
123T VAL* 3.9 18.4 - - + +
124T ASN* 1.3 76.6 - - - +
126T THR* 1.3 63.6 + - - +
127T VAL 4.2 0.2 - - - -
155T LEU* 4.3 26.2 - - + -
174T GLU* 3.2 4.9 - - - -
175T PHE* 2.7 52.2 + - + +
177T ILE* 4.6 2.5 - - + -
187T PHE* 4.3 20.9 - - + -
189T VAL* 4.8 2.5 - - + -
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Residues in contact with THR 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T ILE* 3.6 3.6 - - - +
114T GLN* 2.7 51.6 + - - +
115T SER* 2.9 28.8 + - - +
124T ASN* 2.9 20.5 + - - -
125T VAL* 1.3 72.8 - - - +
127T VAL* 1.3 65.1 + - - +
173T ASN* 3.4 9.4 - - + +
174T GLU* 3.3 20.3 - - + +
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Residues in contact with VAL 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T PRO* 4.1 12.1 - - + -
112T THR 3.7 11.2 - - - +
113T ILE* 4.6 1.8 - - - +
114T GLN* 4.0 1.9 + - - -
126T THR* 1.3 80.6 - - - +
128T GLU* 1.3 77.1 + - - +
129T ASP* 3.5 1.9 + - - +
153T TYR* 3.9 34.3 - - + -
173T ASN* 2.7 37.0 + - + +
175T PHE* 3.7 30.7 - - + -
189T VAL* 4.0 18.6 - - + -
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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