Contacts of the helix formed by residues 589 - 601 (chain B) in PDB entry 6GYS
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 589 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588B SER* 1.3 73.3 + - - +
590B PHE* 1.3 69.0 + - + +
592B THR* 3.3 26.0 + - - +
593B ILE* 3.8 15.5 + - - +
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Residues in contact with PHE 590 (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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527B LEU* 3.6 26.9 - - + -
534B TYR* 3.5 28.0 - + + -
535B HIS* 3.5 31.4 - - - -
536B PRO* 3.7 30.2 - - + +
539B LYS* 4.5 22.0 - - + -
588B SER* 3.2 17.2 + - - +
589B ASP* 1.3 82.5 - - + +
591B ARG* 1.3 56.3 + - + +
593B ILE* 3.2 4.9 + - - +
594B VAL* 2.9 33.3 + - + +
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Residues in contact with ARG 591 (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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539B LYS* 5.8 9.6 - - - +
588B SER* 3.2 40.1 + - - +
590B PHE* 1.3 77.4 - - + +
592B THR* 1.3 57.1 + - - +
594B VAL* 4.3 6.5 - - - -
595B GLU* 2.9 55.1 + - - +
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Residues in contact with THR 592 (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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588B SER 4.0 6.4 + - - -
589B ASP* 3.3 23.1 + - - +
591B ARG* 1.3 78.9 - - - +
593B ILE* 1.3 65.1 + - + +
595B GLU* 3.8 3.6 - - - +
596B GLU* 2.9 42.2 + - + +
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Residues in contact with ILE 593 (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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520B LEU* 3.7 33.4 - - + -
524B VAL* 4.9 14.1 - - + -
536B PRO* 3.7 33.0 - - + -
589B ASP* 4.1 19.5 - - - +
590B PHE 3.2 5.4 + - - +
592B THR* 1.3 80.9 - - + +
594B VAL* 1.3 61.0 + - - +
596B GLU* 3.7 6.9 - - + +
597B PHE* 2.9 30.0 + - - +
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Residues in contact with VAL 594 (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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536B PRO* 3.9 7.6 - - + +
539B LYS* 3.8 37.7 - - + +
540B ILE* 3.9 26.5 - - + +
543B ASN* 5.2 3.6 - - - +
590B PHE 2.9 21.0 + - - +
591B ARG* 3.9 6.1 - - - +
593B ILE* 1.3 77.2 - - - +
595B GLU* 1.3 62.6 + - + +
597B PHE* 3.3 3.3 + - - +
598B GLN* 2.8 52.1 + - - +
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Residues in contact with GLU 595 (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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591B ARG* 2.9 40.0 + - - +
592B THR* 4.0 3.0 - - - +
594B VAL* 1.3 80.0 - - + +
596B GLU* 1.3 61.1 + - - +
598B GLN* 3.7 12.4 - - - +
599B SER* 2.8 29.1 + - - -
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Residues in contact with GLU 596 (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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592B THR* 2.9 32.1 + - + +
593B ILE* 3.7 7.9 - - + +
594B VAL 3.3 0.2 - - - -
595B GLU* 1.3 78.6 - - + +
597B PHE* 1.3 57.4 + - - +
599B SER* 2.3 30.7 + - - -
600B GLU* 2.9 15.0 + - - +
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Residues in contact with PHE 597 (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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513B ARG* 3.6 61.2 - - + -
516B LYS* 3.8 17.7 - - + -
517B LEU* 4.2 15.0 - - + -
520B LEU* 4.3 14.6 - - + -
540B ILE* 3.7 27.4 - - + -
593B ILE 2.9 16.7 + - - +
594B VAL 3.9 2.5 - - - +
596B GLU* 1.3 78.1 - - - +
598B GLN* 1.3 54.5 + - + +
600B GLU* 4.6 6.7 - - - -
601B TYR* 2.6 66.5 + + + +
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Residues in contact with GLN 598 (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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513B ARG* 5.0 8.5 - - - +
540B ILE* 5.1 6.5 + - + +
543B ASN* 5.1 9.1 - - - +
544B ASP* 4.2 8.7 + - - -
547B ILE* 3.9 26.2 - - - +
594B VAL* 2.8 38.4 + - + +
595B GLU* 4.0 12.5 - - - +
597B PHE* 1.3 76.1 - - + +
599B SER* 1.3 61.0 + - - +
601B TYR 3.3 9.6 - - - +
602B ASN* 3.0 38.0 + - - +
603B ILE* 5.7 1.1 - - + +
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Residues in contact with SER 599 (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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595B GLU 2.8 14.9 + - - -
596B GLU* 2.3 39.2 + - - -
598B GLN* 1.3 79.7 - - - +
600B GLU* 1.3 64.2 + - - +
602B ASN* 4.5 2.4 + - - +
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Residues in contact with GLU 600 (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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516B LYS* 5.4 5.5 + - - +
596B GLU 2.9 11.8 + - - +
597B PHE* 4.1 6.6 - - - +
599B SER* 1.3 83.0 + - - +
601B TYR* 1.3 99.7 + - + +
602B ASN 4.1 0.2 - - - -
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Residues in contact with TYR 601 (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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509B TYR* 3.4 28.3 - + - +
512B GLU* 2.6 41.6 + - + -
513B ARG* 3.7 18.5 + - + -
516B LYS* 3.3 38.3 - - + -
597B PHE* 2.6 57.7 + + + +
598B GLN* 3.3 7.5 - - - -
600B GLU* 1.3 107.8 + - + +
602B ASN* 1.3 64.1 + - - +
603B ILE 3.7 1.2 + - - -
605B ASP* 4.7 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