Contacts of the strand formed by residues 1106 - 1110 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1096D LEU* 4.4 1.6 - - + -
1104D LEU* 3.6 33.3 - - + +
1105D GLY* 1.3 80.1 + - - +
1107D GLN* 1.3 82.7 + - - +
1108D ILE* 3.9 13.9 - - + -
1123D ILE* 3.8 26.2 - - + -
1125D SER* 3.2 16.8 - - - +
1126D VAL* 4.4 2.9 - - - -
1127D ALA* 4.6 0.7 - - - +
1132D ALA* 4.2 4.0 - - + -
1138D LEU* 3.6 20.6 - - + -
1144D LEU* 4.2 4.0 - - + -
1164D LEU* 3.6 32.7 - - + +
1173D LEU* 3.7 30.3 - - + -
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Residues in contact with GLN1107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106D PHE* 1.3 89.0 + - - +
1108D ILE* 1.3 65.9 + - - +
1123D ILE* 3.7 6.1 - - - -
1124D SER* 2.9 33.6 + - - +
1125D SER* 3.0 26.1 + - - +
1161D ILE* 5.8 3.6 - - - +
1164D LEU* 6.4 0.2 - - - -
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Residues in contact with ILE1108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106D PHE* 3.9 22.2 - - + -
1107D GLN* 1.3 81.6 + - - +
1109D ILE* 1.3 61.2 + - - +
1121D ILE* 3.8 22.2 - - + -
1122D PHE 3.2 12.8 - - - +
1123D ILE* 4.3 3.6 - - + -
1124D SER* 3.6 6.9 + - - -
1144D LEU* 4.2 5.2 - - + -
1157D HIS* 3.3 22.4 - - + +
1160D ALA* 3.6 31.0 - - + -
1161D ILE* 3.8 29.4 - - + +
1164D LEU* 3.9 17.3 - - + -
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Residues in contact with ILE1109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108D ILE* 1.3 76.2 - - - +
1110D GLY* 1.3 68.7 + - - +
1120D GLY 3.7 0.3 - - - +
1121D ILE* 3.6 2.4 - - - +
1122D PHE* 2.8 53.2 + - + +
1123D ILE 4.7 0.9 - - - +
1124D SER* 3.9 22.0 - - - -
1157D HIS* 4.0 4.3 - - + -
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Residues in contact with GLY1110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D ILE* 1.3 84.5 - - - +
1111D GLY* 1.3 57.3 + - - -
1120D GLY 3.3 10.8 - - - -
1121D ILE* 3.2 9.8 - - - +
1122D PHE* 5.6 0.4 - - - -
1157D HIS* 2.7 38.0 + - - +
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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