Contacts of the helix formed by residues 633 - 648 (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 ASP 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B ASP* 3.0 5.3 + - - +
632B PRO* 1.3 75.7 - - - +
634B THR* 1.3 57.0 + - - +
635B GLU* 3.1 4.7 + - - +
636B GLY* 2.8 22.5 + - - -
637B GLU* 2.7 36.4 + - - +
655B ARG* 4.3 1.2 - - - +
680B LEU* 4.6 8.9 - - - +
809B TYR* 2.6 25.5 + - + +
811B ARG* 2.5 36.1 + - + +
844B HIS* 5.0 6.1 - - + +
974B SER* 4.9 0.7 - - - -
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Residues in contact with THR 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ASP* 1.3 74.3 - - - +
635B GLU* 1.3 56.9 + - - +
637B GLU* 3.2 6.2 + - - +
638B LYS* 2.7 34.8 + - - +
680B LEU* 3.3 31.8 - - + +
683B ALA* 4.0 5.8 - - + -
684B GLN* 3.7 22.3 - - - +
811B ARG* 5.7 0.2 + - - -
972B ARG* 6.0 1.1 + - - +
974B SER* 5.4 3.6 + - - -
1033B GLU* 3.3 33.0 - - + +
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Residues in contact with GLU 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B HIS* 3.7 23.7 + - + +
633B ASP* 3.1 6.0 + - - +
634B THR* 1.3 81.6 + - - +
636B GLY* 1.3 59.6 + - - +
638B LYS* 2.8 20.3 + - - +
639B ILE* 2.9 20.4 + - + +
684B GLN* 2.8 36.2 + - - +
811B ARG* 3.3 29.0 + - - +
974B SER* 5.4 3.1 - - - +
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Residues in contact with GLY 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLU* 4.7 2.0 - - - -
630B THR* 2.6 32.3 + - - -
631B ASP* 3.3 22.4 - - - +
633B ASP* 2.8 13.9 + - - -
635B GLU* 1.3 73.3 - - - +
637B GLU* 1.3 61.7 + - - +
639B ILE* 3.5 7.1 + - - +
640B ALA* 3.1 14.7 + - - +
655B ARG* 3.7 3.4 - - - -
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Residues in contact with GLU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ASP 2.7 19.8 + - - +
634B THR 3.5 4.5 - - - +
636B GLY* 1.3 70.7 - - - +
638B LYS* 1.3 62.5 + - - +
640B ALA* 3.4 1.7 + - - +
641B TRP* 2.9 30.3 + - - +
655B ARG* 2.7 31.0 + - - +
674B ARG* 3.0 27.8 + - - -
676B VAL* 3.2 9.2 - - + +
677B ASP* 2.6 48.8 + - - +
680B LEU* 3.9 20.1 - - + +
681B VAL* 3.8 7.2 - - + -
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Residues in contact with LYS 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B HIS* 4.7 9.3 + - + -
557B VAL* 5.3 2.4 + - - +
578B TYR* 3.3 41.1 + - - -
634B THR 2.7 14.5 + - - +
635B GLU* 2.8 9.8 + - - +
637B GLU* 1.3 76.5 - - - +
639B ILE* 1.3 63.0 + - - +
641B TRP* 3.1 19.8 + - + +
642B ASP* 2.8 54.4 + - - +
681B VAL* 4.0 12.7 - - + +
684B GLN* 2.9 33.9 - - + +
685B VAL* 3.5 17.9 - - + -
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Residues in contact with ILE 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLU* 4.0 19.7 - - + +
552B SER* 4.3 4.7 - - - +
554B GLY* 3.7 31.9 - - - +
555B HIS* 3.4 32.1 - - + +
556B VAL* 4.9 6.5 - - + +
630B THR* 4.0 11.9 - - + -
635B GLU* 2.9 17.0 + - + +
636B GLY* 3.8 10.1 - - - +
638B LYS* 1.3 76.5 - - - +
640B ALA* 1.3 57.3 + - - +
642B ASP* 2.9 14.3 + - - +
643B LEU* 2.9 46.7 + - + +
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Residues in contact with ALA 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B VAL* 3.3 38.9 - - + +
636B GLY 3.1 15.0 + - - +
637B GLU 3.7 4.0 - - - +
639B ILE* 1.3 80.0 - - - +
641B TRP* 1.3 57.1 + - - +
643B LEU* 3.7 4.3 + - - +
644B LYS* 2.9 27.2 + - - +
653B VAL* 4.9 0.3 - - - +
655B ARG* 3.6 22.7 - - - -
676B VAL* 4.1 9.8 - - + +
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Residues in contact with TRP 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.8 28.9 - - + -
21B ALA 5.6 3.4 - - - -
578B TYR* 4.5 11.4 - + - -
637B GLU 2.9 17.8 + - - +
638B LYS* 3.4 22.4 - - + +
640B ALA* 1.3 74.0 - - - +
642B ASP* 1.3 93.8 + - - +
644B LYS* 3.1 12.8 + - + +
645B ASN* 3.0 53.3 + - - +
676B VAL* 3.8 14.8 - - + -
678B GLU* 3.7 31.8 + - - -
681B VAL* 3.5 33.2 - - + -
685B VAL* 4.9 4.3 - - + -
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Residues in contact with ASP 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B HIS* 4.6 6.2 + - - -
556B VAL* 3.7 24.8 - - + +
557B VAL* 4.4 15.7 - - + +
578B TYR* 4.9 2.9 - - - -
638B LYS* 2.8 49.4 + - - +
639B ILE* 3.2 13.9 + - - +
641B TRP* 1.3 89.5 - - - +
643B LEU* 1.3 51.4 + - - +
645B ASN* 2.8 13.9 + - - +
646B LEU* 2.7 40.8 + - + +
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Residues in contact with LEU 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ILE* 4.0 30.1 - - + -
552B SER* 5.1 1.3 - - - -
556B VAL* 3.6 28.3 - - + -
613B ILE* 5.0 3.1 - - + -
616B LEU* 3.9 20.6 - - + -
628B VAL* 4.0 26.0 - - + -
630B THR* 5.2 0.2 - - + -
639B ILE* 2.9 34.8 + - + +
640B ALA* 3.8 4.3 - - - +
642B ASP* 1.3 76.1 - - - +
644B LYS* 1.3 63.8 + - - +
646B LEU* 4.3 5.8 - - + +
647B LEU* 2.9 43.3 + - + +
653B VAL* 5.0 0.9 - - + -
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B ALA 2.9 16.0 + - - +
641B TRP* 3.3 16.6 - - + +
642B ASP 3.1 0.4 - - - -
643B LEU* 1.3 75.4 - - - +
645B ASN* 1.3 61.7 + - - +
647B LEU 3.9 0.2 - - - -
648B SER* 3.0 39.8 + - - +
653B VAL* 3.5 38.6 + - + +
675B ASP* 3.3 28.7 + - - +
676B VAL* 3.8 28.7 - - + +
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Residues in contact with ASN 645 (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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5B ALA* 4.7 19.6 - - + +
20B ALA* 5.2 4.7 - - - +
641B TRP* 3.0 63.7 + - - -
642B ASP* 2.8 9.6 + - - +
644B LYS* 1.3 82.3 - - - +
646B LEU* 1.3 64.5 + - + +
647B LEU 3.5 0.2 + - - -
648B SER* 3.7 12.7 + - - +
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Residues in contact with LEU 646 (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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10B ALA* 5.7 5.4 - - + -
15B ALA* 4.7 13.5 - - + -
18B ALA* 4.9 17.5 - - + -
556B VAL* 4.3 16.2 - - + -
557B VAL* 4.8 11.4 - - + -
613B ILE* 3.4 41.7 - - + -
617B ARG* 3.2 41.2 + - - +
642B ASP* 2.7 21.4 + - + +
643B LEU* 4.1 5.8 - - - +
645B ASN* 1.3 77.0 - - + +
647B LEU* 1.3 62.9 + - + +
648B SER 3.6 1.4 - - - +
650B CYS* 5.4 0.2 - - - -
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Residues in contact with LEU 647 (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* 4.9 0.2 - - + -
510B ILE* 4.4 14.6 - - + -
613B ILE* 4.7 4.0 - - + +
616B LEU* 3.8 13.5 - - + +
617B ARG* 3.8 34.3 - - + +
620B ALA* 4.2 20.0 - - + -
626B VAL* 4.4 21.5 - - + -
643B LEU* 2.9 30.5 + - + +
644B LYS 3.9 0.4 - - - -
646B LEU* 1.3 86.6 - - + +
648B SER* 1.3 68.9 + - - +
650B CYS* 3.1 27.6 + - - +
651B GLY 4.3 3.1 + - - +
653B VAL* 4.8 11.8 - - + +
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Residues in contact with SER 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA* 5.2 13.7 - - - -
6B ALA 6.0 0.7 - - - -
34B LEU* 4.4 14.0 - - - +
35B CYS* 4.5 2.9 - - - +
644B LYS* 3.0 26.9 + - - +
645B ASN* 3.7 10.3 + - - +
646B LEU 3.6 3.0 - - - +
647B LEU* 1.3 80.0 - - - +
649B GLY* 1.3 60.3 + - - +
650B CYS* 3.7 0.3 + - - -
651B GLY 5.0 5.7 + - - -
653B VAL* 5.2 3.0 - - - +
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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
------------------------------------------------------------
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