Contacts of the strand formed by residues 734 - 740 (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 ARG 734 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B SER 3.4 14.6 + - - -
732B ARG* 3.2 23.7 + - - +
733B GLU* 1.3 78.9 - - - +
735B ARG* 1.3 60.4 + - - +
949B SER* 3.5 36.5 + - - +
950B VAL 3.5 11.7 - - - +
951B PRO* 3.5 24.5 - - - +
952B LYS* 4.1 2.5 - - - +
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Residues in contact with ARG 735 (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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734B ARG* 1.3 75.1 - - - +
736B LYS* 1.3 62.1 + - - +
737B ILE* 4.0 13.6 - - + +
748B GLU* 4.0 28.1 + - - +
948B LYS 3.5 0.3 - - - +
949B SER* 3.5 5.3 - - - -
950B VAL* 3.2 40.6 + - - +
951B PRO 3.5 17.3 + - - -
952B LYS* 3.3 31.4 + - + +
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Residues in contact with LYS 736 (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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735B ARG* 1.3 73.7 - - - +
737B ILE* 1.3 61.6 + - - +
748B GLU* 3.1 45.1 + - + +
749B HIS* 3.1 26.0 - - - +
750B ASP* 3.1 36.9 + - - +
909B LYS* 3.3 29.3 - - - +
947B VAL* 5.5 4.0 - - + -
948B LYS 4.2 2.7 - - - -
949B SER* 4.8 3.6 - - - +
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Residues in contact with ILE 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B ARG* 4.0 16.4 - - + +
736B LYS* 1.3 78.4 - - - +
738B ALA* 1.3 55.3 + - - +
739B ILE* 3.4 23.8 - - + -
746B VAL* 4.2 17.0 - - + -
747B LEU 3.2 8.5 - - - +
748B GLU* 5.2 3.4 - - + -
749B HIS 4.0 2.2 - - - -
947B VAL* 2.7 14.4 - - - +
948B LYS* 2.6 51.9 + - + +
950B VAL* 3.3 43.7 - - + -
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Residues in contact with ALA 738 (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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737B ILE* 1.3 77.3 - - - +
739B ILE* 1.3 61.6 + - - +
740B VAL 3.3 6.1 + - - -
746B VAL* 3.4 1.9 - - - -
747B LEU* 2.5 59.6 + - + +
749B HIS* 4.0 12.1 - - + +
751B GLU 4.5 1.6 - - - +
754B PHE* 4.7 1.1 - - + -
945B ALA* 4.0 14.8 - - + -
947B VAL* 3.7 16.8 - - + +
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Residues in contact with ILE 739 (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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737B ILE* 3.4 34.1 - - + -
738B ALA* 1.3 70.6 - - - +
740B VAL* 1.3 65.7 + - - +
741B ARG* 2.9 13.2 + - + +
745B LEU 3.7 10.1 - - - +
746B VAL* 4.2 16.6 - - + +
945B ALA* 3.3 14.8 - - - -
946B GLU* 3.3 17.4 + - + +
947B VAL 3.9 5.3 - - - +
948B LYS* 3.5 26.9 - - + -
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Residues in contact with VAL 740 (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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738B ALA 3.3 0.4 + - - -
739B ILE* 1.3 72.3 - - - +
741B ARG* 1.3 64.8 + - - +
742B ASP 3.4 2.3 + - - -
743B PHE* 3.4 40.2 + - + +
744B ASP 4.1 3.5 + - - -
745B LEU* 3.0 26.0 + - + +
747B LEU* 4.1 18.8 - - + -
754B PHE* 3.8 28.3 - - + -
756B LEU* 4.0 16.6 - - + -
943B VAL* 3.8 21.8 - - + -
944B LYS 3.6 5.2 - - - -
945B ALA* 4.0 1.1 - - - -
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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