Contacts of the strand formed by residues 113 - 119 (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 ILE 113 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112T THR* 1.3 79.4 - - - +
114T GLN* 1.3 63.9 + - - +
115T SER* 3.7 19.7 - - - +
116T PHE* 4.3 14.4 - - + -
125T VAL* 4.0 13.5 - - + -
126T THR 3.8 2.9 - - - -
127T VAL* 4.6 2.0 - - - +
187T PHE* 3.5 43.5 - - + +
188T SER* 3.8 8.5 - - - +
189T VAL* 3.9 18.2 - - + -
205T SER* 3.7 15.9 - - - +
206T PRO* 4.1 3.9 + - - +
208T GLU* 4.0 26.3 - - + +
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Residues in contact with GLN 114 (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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112T THR* 3.2 6.4 + - - -
113T ILE* 1.3 73.2 - - - +
115T SER* 1.3 67.6 + - - +
126T THR* 2.7 35.7 + - + +
127T VAL 4.7 0.2 + - - -
128T GLU* 3.6 43.1 + - + +
129T ASP* 4.5 4.2 - - - +
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Residues in contact with SER 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113T ILE* 3.4 7.3 - - - +
114T GLN* 1.3 86.7 + - - +
116T PHE* 1.3 74.9 + - - +
117T GLU* 5.8 1.4 - - - +
124T ASN* 5.4 0.7 + - - -
125T VAL* 3.6 1.6 - - - -
126T THR* 2.9 38.4 + - - +
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Residues in contact with PHE 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113T ILE* 4.3 10.3 - - + -
115T SER* 1.3 84.8 - - - +
117T GLU* 1.3 61.4 + - - +
123T VAL* 4.1 11.9 - - + -
124T ASN* 3.0 12.3 - - - +
125T VAL* 4.2 5.6 - - + -
187T PHE* 3.9 17.5 - + + -
208T GLU* 3.9 25.6 - - + -
209T CYS 3.3 22.7 - - - -
210T MET* 3.9 35.7 - - + -
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Residues in contact with GLU 117 (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* 5.8 2.0 - - - +
116T PHE* 1.3 76.1 - - - +
118T GLN* 1.3 67.2 + - - +
119T VAL* 3.2 29.8 + - + +
123T VAL* 3.2 3.0 - - - -
124T ASN* 2.6 48.0 + - + +
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Residues in contact with GLN 118 (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* 6.0 0.2 - - - -
117T GLU* 1.3 77.4 - - - +
119T VAL* 1.3 57.2 + - - +
120T GLY 3.2 22.1 + - - +
121T THR* 3.3 5.0 - - - -
122T LYS 2.8 31.2 + - - +
123T VAL* 3.9 8.9 - - - +
179T VAL* 3.5 19.3 - - - +
180T ASP 5.3 3.0 + - - -
181T LYS* 6.2 0.8 - - - +
182T GLY 5.7 3.6 - - - +
210T MET* 3.9 21.4 - - + +
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Residues in contact with VAL 119 (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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117T GLU* 3.5 39.9 - - - +
118T GLN* 1.3 68.8 - - - +
120T GLY* 1.3 66.2 + - - +
121T THR 3.3 0.5 + - - -
122T LYS* 2.7 27.2 + - - +
124T ASN* 4.0 17.7 - - + +
176T LEU* 5.2 7.1 - - + +
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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