Contacts of the helix formed by residues 633 - 644 (chain A) in PDB entry 1HKC
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 VAL 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A PHE* 4.0 12.3 - - + -
600A PHE* 4.3 12.3 - - + -
602A PHE* 3.4 48.2 - - + -
614A GLY* 3.1 20.5 + - - +
616A LEU* 4.2 16.6 - - + +
619A TRP* 5.8 0.4 - - + -
628A CYS* 5.4 1.1 - - + +
631A HIS 3.4 2.3 + - - +
632A ASP* 1.3 71.0 - - - +
634A VAL* 1.3 64.8 + - + +
636A LEU* 3.1 15.4 + - + +
637A LEU* 3.0 22.3 + - - +
654A VAL* 4.4 18.8 - - + -
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Residues in contact with VAL 634 (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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600A PHE* 4.5 9.6 - - + -
612A ASP* 3.1 36.1 - - - +
613A ALA* 4.2 4.3 - - - +
632A ASP* 3.1 7.6 + - - +
633A VAL* 1.3 77.6 - - + +
635A THR* 1.3 57.7 + - - +
637A LEU* 3.4 6.0 + - + +
638A ARG* 2.9 53.0 + - - +
651A VAL* 3.7 23.8 - - + -
654A VAL* 3.9 26.7 - - + -
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Residues in contact with THR 635 (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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632A ASP* 2.8 27.4 + - - +
634A VAL* 1.3 76.3 - - - +
636A LEU* 1.3 67.0 + - + +
638A ARG* 4.3 12.7 + - - +
639A ASP* 2.8 50.2 + - - +
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Residues in contact with LEU 636 (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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571A GLY 4.7 3.4 - - - +
575A PHE* 3.4 41.8 - - + +
627A ASP 4.1 7.6 - - - +
628A CYS* 3.8 33.0 - - + +
631A HIS* 4.2 20.0 - - + -
632A ASP 3.1 13.7 + - - +
633A VAL* 3.1 14.0 + - + +
635A THR* 1.3 83.0 - - + +
637A LEU* 1.3 58.1 + - - +
639A ASP* 3.5 8.5 + - + +
640A ALA* 3.1 26.9 + - - +
643A ARG* 3.9 3.6 + - - +
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 4.5 9.4 - - + -
575A PHE* 3.9 21.0 - - + -
578A ILE* 4.5 15.0 - - + -
579A VAL* 4.0 20.6 - - + -
582A ILE* 4.6 6.3 - - + -
598A LEU* 4.5 14.8 - - + -
600A PHE* 4.0 24.9 - - + -
633A VAL 3.0 12.8 + - - +
634A VAL* 3.6 7.2 - - - +
636A LEU* 1.3 75.1 - - - +
638A ARG* 1.3 65.4 + - - +
640A ALA* 3.0 4.4 + - - +
641A ILE* 2.9 36.4 + - + +
651A VAL* 3.9 24.2 - - + -
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Residues in contact with ARG 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ASP* 2.9 35.1 + - - +
632A ASP* 5.2 1.4 + - - -
634A VAL* 2.9 36.1 + - - +
635A THR* 3.8 14.3 + - - +
637A LEU* 1.3 76.4 - - - +
639A ASP* 1.3 66.6 + - - +
641A ILE* 3.3 11.6 + - + +
642A LYS* 3.1 24.3 + - - +
649A LEU 6.0 0.9 - - - +
650A ASP* 5.7 0.2 + - - -
651A VAL* 3.0 44.8 + - + +
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Residues in contact with ASP 639 (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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635A THR* 2.8 37.8 + - - +
636A LEU* 3.6 7.4 - - - +
638A ARG* 1.3 80.3 - - - +
640A ALA* 1.3 61.7 + - - +
642A LYS* 3.6 23.6 + - - +
643A ARG* 3.1 40.7 + - - +
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Residues in contact with ALA 640 (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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575A PHE* 3.1 37.7 - - + +
576A ASP* 3.8 5.3 - - - +
579A VAL* 3.7 8.1 - - + +
636A LEU 3.1 10.8 + - - +
637A LEU 3.0 8.5 + - - +
639A ASP* 1.3 73.0 - - - +
641A ILE* 1.3 67.3 + - - +
643A ARG* 3.0 37.3 + - - +
644A ARG* 3.4 8.7 + - - +
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Residues in contact with ILE 641 (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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579A VAL* 3.8 23.5 - - + +
582A ILE* 5.9 0.7 - - + -
637A LEU* 2.9 32.6 + - + +
638A ARG* 3.6 13.9 - - + +
639A ASP 3.3 0.2 - - - -
640A ALA* 1.3 76.2 - - - +
642A LYS* 1.3 62.4 + - - +
644A ARG* 3.1 15.4 + - - +
645A GLU 3.3 8.8 + - - -
647A PHE* 3.5 32.6 - - + +
648A ASP* 4.3 18.2 - - - +
649A LEU* 4.0 36.8 - - + +
651A VAL* 4.5 9.6 - - + -
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Residues in contact with LYS 642 (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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638A ARG 3.1 13.6 + - - +
639A ASP* 3.9 25.3 + - - +
641A ILE* 1.3 79.1 - - - +
643A ARG* 1.3 68.8 + - - +
644A ARG 3.2 0.9 + - - -
645A GLU* 3.3 26.7 + - + +
647A PHE 5.7 0.4 - - - -
648A ASP* 5.9 1.3 - - - +
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Residues in contact with ARG 643 (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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572A GLU* 3.3 41.1 + - - +
575A PHE* 5.4 1.2 - - - +
576A ASP* 2.6 44.8 + - - +
636A LEU* 3.9 4.2 + - - +
639A ASP* 3.1 24.9 + - - +
640A ALA* 3.0 44.1 - - - +
642A LYS* 1.3 81.9 - - - +
644A ARG* 1.3 60.1 + - - +
645A GLU* 4.8 2.1 - - - +
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Residues in contact with ARG 644 (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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576A ASP 5.0 2.6 + - - -
579A VAL* 3.7 24.2 - - + -
580A SER* 3.6 27.4 + - - +
583A SER* 3.3 19.3 + - - -
640A ALA 3.4 6.8 + - - +
641A ILE 3.1 10.7 + - - +
642A LYS 3.1 0.6 - - - -
643A ARG* 1.3 79.5 - - - +
645A GLU* 1.3 65.2 + - - +
646A GLU* 2.6 45.6 + - + +
647A PHE* 4.2 8.1 - - + +
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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