Contacts of the helix formed by residues 654 - 666 (chain A) in PDB entry 6QVC
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 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A LEU* 2.8 10.3 + - - +
629A LEU* 2.5 39.3 + - + +
632A THR* 2.2 46.4 + - - -
633A THR* 4.1 12.4 + - - +
634A VAL 3.2 28.7 - - - +
635A LYS* 2.9 10.5 + - - +
636A THR* 4.1 0.2 - - - +
637A LEU* 3.9 24.3 - - + +
652A VAL 3.5 3.2 + - - -
653A GLU* 1.3 71.5 - - - +
655A SER* 1.3 60.0 + - - +
657A LEU* 3.1 9.0 + - + +
658A GLN* 2.9 54.1 + - + +
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Residues in contact with SER 655 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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635A LYS 4.3 3.2 + - - -
653A GLU* 4.0 14.9 + - - +
654A ARG* 1.3 78.5 - - - +
656A GLU* 1.3 59.6 + - - +
658A GLN* 3.4 19.5 - - - +
659A ALA* 2.9 27.9 + - - +
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Residues in contact with GLU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A VAL* 5.7 2.9 - - + -
653A GLU* 3.7 25.8 + - + +
654A ARG 3.2 0.6 - - - -
655A SER* 1.3 78.0 + - - +
657A LEU* 1.3 63.0 + - + +
659A ALA* 3.2 13.0 + - - +
660A LEU* 2.9 51.1 + - + +
663A ARG* 4.8 7.0 + - - -
818A SER* 5.5 5.4 + - - +
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A VAL* 5.5 5.4 - - + -
628A LEU* 6.5 0.4 - - + -
629A LEU* 5.8 1.8 - - + -
637A LEU* 3.8 28.0 - - + -
652A VAL* 3.7 22.9 - - + -
653A GLU 3.5 15.9 + - - +
654A ARG* 3.1 7.7 + - + +
656A GLU* 1.3 74.3 - - + +
658A GLN* 1.3 58.5 + - + +
660A LEU* 3.3 19.1 + - + +
661A LEU* 2.9 44.4 + - + +
819A CYS* 5.8 7.4 - - - -
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Residues in contact with GLN 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A LEU* 3.8 26.6 - - + +
654A ARG* 2.9 52.9 + - + +
655A SER* 3.4 21.9 - - - +
657A LEU* 1.3 76.0 - - - +
659A ALA* 1.3 56.3 + - - +
661A LEU* 4.7 0.4 - - - -
662A GLN* 2.9 52.5 + - - +
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Residues in contact with ALA 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A SER 2.9 14.0 + - - +
656A GLU* 3.4 18.2 - - - +
657A LEU 3.2 0.2 - - - -
658A GLN* 1.3 76.7 - - - +
660A LEU* 1.3 57.1 + - - +
662A GLN* 5.1 2.0 - - - -
663A ARG* 2.9 68.8 + - - +
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A GLU* 2.9 42.1 + - + +
657A LEU* 3.3 19.9 + - + +
659A ALA* 1.3 76.2 - - + +
661A LEU* 1.3 60.9 + - + +
663A ARG* 3.7 3.8 - - - +
664A HIS* 2.9 32.6 + - - +
818A SER* 4.9 17.9 - - - +
819A CYS* 5.3 18.2 - - + +
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Residues in contact with LEU 661 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A LEU* 4.4 33.2 - - + +
626A ARG* 6.3 0.7 - - + -
629A LEU* 3.7 41.5 - - + -
657A LEU* 2.9 26.6 + - + +
658A GLN 4.0 2.9 - - - +
660A LEU* 1.3 78.2 - - + +
662A GLN* 1.3 56.8 + - + +
664A HIS* 3.2 4.0 + - + +
665A LEU* 2.9 44.7 + - + +
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Residues in contact with GLN 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A LEU* 5.5 11.3 - - + +
658A GLN* 2.9 36.4 + - - +
659A ALA* 4.4 2.3 - - - +
661A LEU* 1.3 79.7 - - + +
663A ARG* 1.3 60.6 + - + +
664A HIS 3.2 0.2 - - - -
665A LEU* 3.1 12.0 + - + +
666A CYS* 3.0 38.0 + - - -
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Residues in contact with ARG 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A GLU* 4.8 8.3 + - - -
659A ALA* 2.9 43.4 + - - +
660A LEU* 3.7 4.9 - - - +
662A GLN* 1.3 76.4 - - + +
664A HIS* 1.3 57.1 + - - +
666A CYS* 5.0 3.6 - - + -
667A PRO* 3.3 22.1 - - + +
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Residues in contact with HIS 664 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A LEU 2.9 20.4 + - - +
661A LEU* 3.8 4.0 - - + +
663A ARG* 1.3 76.9 - - - +
665A LEU* 1.3 65.9 + - + +
666A CYS 3.3 1.8 - - - -
667A PRO* 3.4 12.6 - - - +
668A GLU* 3.2 47.0 + - + +
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Residues in contact with LEU 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A ARG* 4.1 24.2 - - + +
629A LEU* 6.6 0.2 - - + -
661A LEU* 2.9 35.9 + - + +
662A GLN* 3.1 13.9 + - + +
664A HIS* 1.3 81.2 - - + +
666A CYS* 1.3 63.1 + - - +
668A GLU* 3.3 37.2 - - - +
669A ARG* 4.4 9.2 - - - +
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Residues in contact with CYS 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A GLN* 3.0 21.8 + - - +
663A ARG* 5.0 2.9 - - + -
665A LEU* 1.3 81.4 - - - +
667A PRO* 1.3 63.4 - - + +
668A GLU 3.1 9.7 + - - +
669A ARG* 4.7 6.3 - - - +
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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