Contacts of the strand formed by residues 625 - 628 (chain B) in PDB entry 1GKU
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 PHE 625 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505B LYS* 6.3 0.4 - - + -
506B PRO 3.8 12.3 - - - +
507B ALA* 3.5 20.2 - - + -
508B LEU 2.9 22.5 + - - -
545B TYR* 3.4 40.2 - + - -
620B ALA 4.2 0.8 + - - -
623B ALA* 2.9 6.9 - - - +
624B GLU* 1.3 81.9 - - - +
626B VAL* 1.3 62.9 + - - +
627B ILE* 3.7 16.4 - - + -
652B ALA* 3.6 24.2 - - + -
654B LYS* 4.0 21.5 - - + -
673B LEU* 3.9 18.4 - - + -
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Residues in contact with VAL 626 (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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508B LEU* 3.3 15.9 - - + +
510B ILE* 3.9 26.5 - - + -
620B ALA* 3.7 34.5 - - + +
624B GLU 5.4 0.4 - - - -
625B PHE* 1.3 79.9 - - - +
627B ILE* 1.3 74.3 + - - +
628B VAL* 4.4 7.9 - - + -
647B LEU* 4.4 8.7 - - + -
650B CYS* 5.9 0.9 - - + -
651B GLY 5.7 1.8 - - - +
652B ALA 2.8 15.5 + - - +
653B VAL* 3.5 19.0 - - + -
654B LYS* 3.0 26.0 + - - +
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Residues in contact with ILE 627 (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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507B ALA* 4.3 10.1 - - + -
508B LEU 2.6 13.3 + - - +
509B PHE* 3.2 20.4 - - + -
510B ILE* 2.8 26.0 + - - +
545B TYR* 4.0 9.6 - - + -
547B LEU* 5.3 1.3 - - + -
625B PHE* 3.7 33.2 - - + -
626B VAL* 1.3 80.3 - - - +
628B VAL* 1.3 65.2 + - - +
629B GLY 3.8 0.2 + - - -
654B LYS* 3.4 7.2 - - + +
656B ALA* 3.4 30.7 - - + +
670B LEU* 3.8 23.1 - - + -
673B LEU* 4.2 14.4 - - + -
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Residues in contact with VAL 628 (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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510B ILE* 3.7 10.5 - - + +
626B VAL* 4.4 8.1 - - + -
627B ILE* 1.3 74.5 - - - +
629B GLY* 1.3 60.2 + - - +
630B THR* 3.7 17.9 - - + +
640B ALA* 3.3 40.4 - - + +
643B LEU* 4.0 21.5 - - + -
653B VAL* 4.1 20.6 - - + -
654B LYS 2.9 16.0 + - - +
655B ARG* 3.2 11.7 + - - -
656B ALA 3.0 23.3 + - - -
676B VAL* 6.3 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