Contacts of the strand formed by residues 1106 - 1109 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096B LEU* 4.1 3.1 - - + -
1102B TYR 4.8 0.2 + - - -
1104B LEU* 3.5 47.8 - - + +
1105B GLY* 1.3 79.5 + - - +
1107B GLN* 1.3 76.6 + - - +
1108B ILE* 3.7 23.3 - - + +
1123B ILE* 3.6 24.0 - - + -
1125B SER 3.3 14.8 - - - +
1126B VAL* 4.1 5.6 - - + +
1127B ALA* 4.7 0.7 - - - +
1132B ALA* 4.0 2.5 - - + -
1138B LEU* 3.4 27.6 - - + -
1144B LEU* 4.7 4.9 - - + -
1164B LEU* 4.1 17.6 - - + +
1173B LEU* 4.0 22.0 - - + -
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Residues in contact with GLN1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B TYR 5.9 1.2 + - - -
1105B GLY* 5.6 0.6 - - - -
1106B PHE* 1.3 90.3 + - - +
1108B ILE* 1.3 67.1 + - - +
1123B ILE* 3.5 9.4 - - - +
1124B SER* 2.9 29.9 + - - +
1125B SER* 3.0 27.6 + - - +
1161B ILE* 5.4 6.4 - - - +
1116C ARG* 6.4 0.7 - - + -
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Residues in contact with ILE1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B PHE* 3.7 26.0 - - + -
1107B GLN* 1.3 83.5 + - - +
1109B ILE* 1.3 69.9 + - - +
1121B ILE* 3.8 19.1 - - + -
1122B PHE 3.2 11.4 - - - +
1123B ILE* 4.1 5.8 - - + -
1124B SER* 4.0 1.3 + - - -
1144B LEU* 4.6 1.3 - - + -
1157B HIS* 2.9 23.1 + - + +
1160B ALA* 3.8 26.0 - - + -
1161B ILE* 3.7 32.3 - - + +
1164B LEU* 3.7 24.7 - - + -
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Residues in contact with ILE1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A ILE* 3.5 33.9 - - + +
1110A GLY* 5.2 5.4 - - - -
1120A GLY* 5.2 3.1 - - - +
1122A PHE* 3.4 42.6 - - + -
1108B ILE* 1.3 78.8 - - - +
1110B GLY* 1.3 58.7 + - - +
1120B GLY 3.6 1.7 - - - +
1121B ILE* 3.6 4.5 - - - +
1122B PHE* 2.8 36.6 + - + +
1123B ILE 4.8 1.6 - - - +
1124B SER* 3.6 25.1 - - - +
1157B HIS* 3.4 11.4 - - - +
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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