Contacts of the strand formed by residues 1106 - 1109 (chain A) in PDB entry 5GLJ
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 PHE1106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096A LEU* 4.3 2.7 - - + -
1102A TYR 4.9 0.2 + - - -
1104A LEU* 3.5 36.4 - - + +
1105A GLY* 1.3 79.4 + - - +
1107A GLN* 1.3 70.7 + - - +
1108A ILE* 3.8 13.9 - - + -
1123A ILE* 3.6 27.8 - - + -
1125A SER 3.2 16.6 - - - +
1126A VAL* 4.3 4.3 - - + -
1132A ALA* 4.1 2.5 - - + -
1138A LEU* 3.4 28.3 - - + -
1144A LEU* 4.8 3.4 - - + -
1164A LEU* 3.8 32.4 - - + +
1173A LEU* 3.8 22.7 - - + -
1202A CL 3.7 4.2 - - - +
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Residues in contact with GLN1107 (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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1106A PHE* 1.3 78.9 - - - +
1108A ILE* 1.3 64.7 + - - +
1123A ILE* 3.5 10.4 - - - +
1124A SER* 2.9 33.4 + - - +
1125A SER* 2.9 27.1 + - - +
1164A LEU* 6.4 0.2 - - - -
1202A CL 3.8 9.8 - - + +
1114D MET 4.3 12.6 + - - +
1115D GLY* 6.0 0.4 - - - -
1116D ARG 4.5 5.8 - - - +
1117D LEU* 3.9 27.4 - - + +
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Residues in contact with ILE1108 (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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1106A PHE* 3.8 23.8 - - + -
1107A GLN* 1.3 84.0 - - - +
1109A ILE* 1.3 71.0 + - - +
1121A ILE* 3.7 19.1 - - + -
1122A PHE 3.2 11.9 - - - +
1123A ILE* 4.0 8.3 - - + -
1124A SER* 3.9 1.5 + - - -
1144A LEU* 4.4 2.7 - - + -
1157A HIS* 3.0 24.1 + - + +
1160A ALA* 3.6 30.7 - - + -
1161A ILE* 3.9 20.8 - - + +
1164A LEU* 3.7 21.8 - - + -
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Residues in contact with ILE1109 (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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1108A ILE* 1.3 80.5 - - - +
1110A GLY* 1.3 60.0 + - - +
1120A GLY 3.6 0.5 - - - +
1121A ILE* 3.5 5.6 - - - +
1122A PHE* 2.9 38.7 + - + +
1123A ILE 4.6 3.1 - - - +
1124A SER* 3.4 24.5 - - - +
1157A HIS* 3.7 11.0 - - + +
1109B ILE* 3.5 23.3 - - + +
1110B GLY* 5.4 5.8 - - - -
1120B GLY* 5.4 1.3 - - - +
1122B PHE* 3.4 52.7 - - + -
1141B GLY* 6.4 0.4 - - - -
1117D LEU* 5.9 0.4 - - + -
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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