Contacts of the helix formed by residues 658 - 673 (chain A) in PDB entry 6UMW
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 SER 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656A GLY 3.6 2.3 + - - -
657A TYR* 1.3 76.3 - - - +
659A GLU* 1.3 65.7 + - - +
660A LYS* 3.2 10.8 + - - +
661A GLN* 2.9 37.1 + - - +
662A ARG* 2.9 21.8 + - - +
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Residues in contact with GLU 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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658A SER* 1.3 74.3 - - - +
660A LYS* 1.3 56.6 + - - +
662A ARG* 3.2 34.3 + - - +
663A ARG* 2.9 41.1 + - - +
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Residues in contact with LYS 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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658A SER* 3.2 8.6 + - - +
659A GLU* 1.3 79.4 - - - +
661A GLN* 1.3 57.2 + - + +
663A ARG* 2.8 49.9 + - - +
664A ASP* 3.0 55.6 + - - +
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Residues in contact with GLN 661 (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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630A PHE* 5.4 6.7 - - + -
653A LEU* 3.8 10.4 - - + +
656A GLY 4.6 1.2 - - - +
657A TYR* 3.4 15.7 - - + -
658A SER* 2.9 41.9 + - - +
660A LYS* 1.3 73.1 - - + +
662A ARG* 1.3 61.0 + - - +
664A ASP* 3.4 10.6 + - - +
665A PHE* 2.8 30.0 + - - +
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Residues in contact with ARG 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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653A LEU* 3.7 11.3 - - - +
657A TYR* 4.0 21.8 + - + -
658A SER 2.9 12.9 + - - +
659A GLU* 3.4 37.3 + - - +
661A GLN* 1.3 75.2 - - - +
663A ARG* 1.3 59.7 + - - +
665A PHE* 3.1 3.6 + - - +
666A LEU* 2.8 45.3 + - + +
688A THR* 3.1 33.5 + - - -
690A SER 5.4 0.2 + - - -
691A ARG* 6.2 2.6 - - - +
693A VAL* 3.2 32.9 - - + +
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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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659A GLU* 2.9 26.7 + - - +
660A LYS* 2.8 58.3 - - - +
662A ARG* 1.3 75.8 - - + +
664A ASP* 1.3 63.0 + - - +
666A LEU* 3.3 6.9 + - - +
667A SER* 2.8 36.8 + - - +
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Residues in contact with ASP 664 (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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630A PHE* 5.0 15.9 - - + -
660A LYS* 3.0 49.4 + - - +
661A GLN* 3.5 9.6 - - - +
663A ARG* 1.3 77.4 + - - +
665A PHE* 1.3 62.8 + - - +
667A SER* 3.3 8.3 + - - -
668A GLU* 3.2 20.1 + - - +
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Residues in contact with PHE 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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630A PHE* 4.3 14.5 - + + -
651A LYS* 3.5 41.5 - - + -
652A THR 4.2 6.3 - - - -
653A LEU* 3.6 30.3 - - + -
661A GLN 2.8 14.7 + - - +
662A ARG 3.1 7.8 + - - +
664A ASP* 1.3 75.5 - - - +
666A LEU* 1.3 69.2 + - + +
668A GLU* 3.1 35.4 + - - +
669A ALA 3.3 4.3 + - - -
693A VAL* 3.8 30.7 - - + -
694A MET* 4.1 4.3 - - - -
695A ILE* 3.5 41.3 - - + +
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Residues in contact with LEU 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 ARG* 2.8 56.4 + - + +
663A ARG* 4.1 5.2 - - - +
665A PHE* 1.3 89.5 - - + +
667A SER* 1.3 57.3 + - - +
669A ALA* 3.2 6.9 + - + +
670A SER* 3.0 28.6 + - - -
686A VAL* 4.7 15.3 - - + -
687A VAL 5.0 0.7 - - - +
688A THR* 3.7 33.4 - - + -
693A VAL* 4.5 7.6 - - + -
694A MET 5.0 0.9 - - - +
695A ILE* 5.0 1.1 - - + -
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Residues in contact with SER 667 (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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663A ARG* 2.8 22.5 + - - +
664A ASP* 3.6 8.2 - - - -
665A PHE 3.2 0.2 - - - -
666A LEU* 1.3 74.9 - - - +
668A GLU* 1.3 66.6 + - - +
670A SER* 3.2 9.5 + - - -
671A ILE* 3.2 29.3 + - - +
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Residues in contact with GLU 668 (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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630A PHE* 3.8 30.6 - - + -
651A LYS* 5.2 4.4 - - - -
664A ASP 3.2 10.3 + - - +
665A PHE* 3.1 25.0 + - - +
667A SER* 1.3 75.7 - - - +
669A ALA* 1.3 63.7 + - - +
671A ILE* 3.0 18.1 + - - +
672A MET* 3.1 28.0 + - - +
695A ILE* 4.1 8.2 - - + +
763A PHE* 3.9 33.0 + - - +
901A CTC 4.4 21.1 + - - -
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Residues in contact with ALA 669 (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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611A ALA* 5.7 2.9 + - + -
665A PHE 3.3 2.0 + - - -
666A LEU* 3.2 15.3 + - + +
668A GLU* 1.3 78.3 - - - +
670A SER* 1.3 62.9 + - - +
671A ILE 3.2 0.2 + - - -
672A MET* 3.2 9.7 + - - +
673A GLY* 3.0 20.3 + - - -
683A LEU* 3.6 13.8 - - + +
686A VAL* 3.6 30.3 - - + -
695A ILE* 3.8 21.5 - - + +
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Residues in contact with SER 670 (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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611A ALA* 5.1 16.2 + - - +
666A LEU 3.0 15.3 + - - -
667A SER* 3.2 13.4 + - - -
669A ALA* 1.3 75.8 - - - +
671A ILE* 1.3 69.4 + - - +
673A GLY* 3.5 7.7 + - - -
674A GLN* 3.7 14.6 + - - +
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Residues in contact with ILE 671 (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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667A SER* 3.2 18.8 - - - +
668A GLU* 3.0 9.6 + - - +
670A SER* 1.3 82.0 - - - +
672A MET* 1.3 67.2 + - + +
674A GLN* 3.1 26.9 + - - +
675A PHE* 3.5 22.3 - - + -
740A TYR* 4.0 35.4 - - + +
763A PHE* 5.6 9.4 - - + -
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Residues in contact with MET 672 (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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668A GLU* 3.1 30.6 + - - +
669A ALA* 3.2 7.8 + - - +
671A ILE* 1.3 76.5 - - - +
673A GLY* 1.3 61.9 + - - +
675A PHE* 3.1 31.5 + - - +
681A ILE 4.4 8.7 - - - +
683A LEU* 3.9 29.3 + - + +
695A ILE* 4.4 10.3 - - - -
697A THR* 3.7 17.7 - - + -
763A PHE* 3.9 24.5 - - + -
901A CTC 2.9 42.8 - - - +
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Residues in contact with GLY 673 (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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611A ALA 4.7 11.7 + - - -
669A ALA 3.0 12.1 + - - -
670A SER 3.5 4.0 + - - -
671A ILE 3.1 0.6 - - - -
672A MET* 1.3 76.6 - - - +
674A GLN* 1.3 59.3 + - - +
675A PHE 3.2 4.9 + - - +
683A LEU* 3.7 22.4 - - - +
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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