Contacts of the helix formed by residues 632 - 647 (chain A) in PDB entry 4KXA
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 GLU 632 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A VAL* 3.4 25.2 + - - +
550A ASN* 3.6 9.0 - - - +
551A GLY* 2.7 26.3 + - - -
552A VAL* 3.0 28.1 + - - +
631A TYR* 1.3 77.8 - - - +
633A VAL* 1.3 66.3 + - - +
634A ALA* 3.2 7.9 - - + +
635A THR* 3.0 25.0 + - - +
636A TRP* 3.1 10.2 + - - -
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Residues in contact with VAL 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A TYR 3.6 1.3 + - - +
632A GLU* 1.3 72.6 - - - +
634A ALA* 1.3 59.0 + - - +
636A TRP* 3.2 10.3 + - - +
637A ASP* 2.9 29.7 + - + +
671A LEU* 4.2 20.2 - - + -
672A ASP* 5.9 2.5 - - + +
675A VAL* 4.0 22.1 - - + +
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Residues in contact with ALA 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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632A GLU* 3.2 5.6 - - + +
633A VAL* 1.3 79.6 - - - +
635A THR* 1.3 57.7 + - - +
637A ASP* 3.3 9.2 + - - +
638A SER* 3.0 31.3 + - - -
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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
----------------------------------------------------------
549A VAL* 5.5 1.6 - - - +
552A VAL* 5.2 9.0 - - - +
616A PHE* 3.9 26.2 - - + -
617A LEU 5.8 0.4 - - - +
631A TYR* 3.7 30.8 - - + +
632A GLU* 3.0 27.1 + - - +
634A ALA* 1.3 75.6 - - - +
636A TRP* 1.3 60.5 + - - +
638A SER* 3.0 9.2 + - - -
639A ILE* 2.9 32.5 + - + +
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Residues in contact with TRP 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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629A VAL 3.6 22.4 - - - -
630A ASN* 3.1 18.8 + - - -
631A TYR* 3.1 41.0 + + - +
632A GLU 3.1 14.7 + - - -
633A VAL* 3.5 7.4 - - - +
635A THR* 1.3 76.4 - - - +
637A ASP* 1.3 62.6 + - - +
639A ILE* 3.2 22.1 + - + +
640A ALA* 3.1 22.5 + - - +
658A LEU* 3.7 37.9 - - + -
661A ASP* 4.5 3.8 - - + -
662A ALA* 4.0 9.9 - - + -
665A LEU* 3.9 13.2 - - + -
671A LEU* 3.6 24.9 - - + +
675A VAL* 3.5 19.9 - - + +
679A LEU* 3.9 30.2 - - + +
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Residues in contact with ASP 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A VAL* 2.9 16.3 + - + +
634A ALA* 3.3 13.4 - - - +
636A TRP* 1.3 75.9 - - - +
638A SER* 1.3 61.2 + - - +
640A ALA* 3.4 9.0 + - - +
641A THR* 3.2 26.1 + - - -
675A VAL* 4.9 5.1 - - + +
678A ASN* 4.7 4.4 + - - +
1D NAG 3.8 25.1 + - - +
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Residues in contact with SER 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A PHE* 5.7 6.7 - - - -
634A ALA 3.0 16.3 + - - -
635A THR* 3.0 11.8 + - - -
637A ASP* 1.3 74.5 + - - +
639A ILE* 1.3 59.9 + - - +
641A THR* 3.4 7.8 + - - -
642A ALA* 2.8 30.6 + - - +
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Residues in contact with ILE 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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616A PHE* 3.8 26.9 - - + -
631A TYR* 4.2 13.7 - - + -
635A THR* 2.9 32.4 + - + +
636A TRP* 3.2 30.3 + - + +
638A SER* 1.3 73.4 - - - +
640A ALA* 1.3 59.8 + - - +
642A ALA* 3.2 7.2 + - - +
643A LEU* 2.9 43.1 + - + +
650A PHE* 4.4 8.7 - - + -
658A LEU* 4.4 23.3 - - + -
679A LEU* 3.9 15.5 - - + -
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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
----------------------------------------------------------
636A TRP 3.1 12.0 + - - +
637A ASP* 3.5 12.1 - - - +
639A ILE* 1.3 76.4 - - - +
641A THR* 1.3 61.8 + - - +
643A LEU* 3.3 8.3 + - - +
644A SER* 3.1 24.7 + - - -
675A VAL 5.4 0.2 - - - +
678A ASN* 3.8 35.9 - - + +
679A LEU* 3.7 15.5 - - + +
682A TYR* 5.2 0.2 - - - +
1D NAG 4.6 9.4 - - + +
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Residues in contact with THR 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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637A ASP* 3.2 15.2 + - - -
638A SER* 3.7 10.0 - - - -
640A ALA* 1.3 76.7 - - - +
642A ALA* 1.3 65.2 + - - +
644A SER* 3.1 9.7 + - - -
645A LEU* 3.0 41.3 + - + +
1D NAG 4.1 12.3 + - - -
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Residues in contact with ALA 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 SER 2.8 19.1 + - - +
639A ILE* 3.6 6.1 - - - +
641A THR* 1.3 76.2 - - - +
643A LEU* 1.3 57.7 + - - +
645A LEU* 3.4 8.5 + - - +
646A ASN 2.9 35.4 + - - +
649A THR* 5.0 6.0 + - + +
650A PHE* 4.2 18.6 - - + -
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Residues in contact with LEU 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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639A ILE* 2.9 36.2 + - + +
640A ALA* 3.6 6.1 - - - +
642A ALA* 1.3 77.6 - - - +
644A SER* 1.3 60.6 + - - +
647A HIS* 3.3 37.8 + - + +
650A PHE* 3.8 26.5 - - + -
655A ARG* 3.9 24.2 - - + -
658A LEU* 5.9 4.5 - - + -
659A ILE* 5.5 5.2 - - + -
679A LEU* 4.2 19.5 - - + +
682A TYR* 3.4 39.2 - - + +
685A ARG* 4.0 2.9 + - - -
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Residues in contact with SER 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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640A ALA 3.1 12.8 + - - -
641A THR* 3.1 12.4 + - - -
643A LEU* 1.3 75.7 - - - +
645A LEU* 1.3 63.4 + - - +
681A LYS* 4.3 10.9 - - - +
682A TYR* 3.8 22.8 + - - +
685A ARG* 3.4 25.7 + - - +
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Residues in contact with LEU 645 (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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641A THR* 3.0 39.6 + - + +
642A ALA* 3.8 6.5 - - - +
643A LEU 4.3 0.2 - - - -
644A SER* 1.3 81.5 - - - +
646A ASN* 1.3 62.7 + - + +
685A ARG* 5.7 0.4 - - - -
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Residues in contact with ASN 646 (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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642A ALA 2.9 15.3 + - - +
645A LEU* 1.3 77.4 - - + +
647A HIS* 1.3 63.5 + - - +
648A LYS* 3.7 19.2 + - - +
649A THR* 2.8 48.4 + - - +
650A PHE* 5.3 0.2 - - - -
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Residues in contact with HIS 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 3.3 31.6 + - + +
646A ASN* 1.3 69.9 + - - +
648A LYS* 1.3 79.2 + - + +
649A THR* 3.0 10.3 + - - -
650A PHE* 3.1 20.4 + - - +
655A ARG* 3.5 21.2 + - - -
682A TYR* 3.4 32.9 - + + -
685A ARG* 3.1 45.8 + - + +
686A GLU* 3.8 12.7 - - - -
687A GLU* 4.5 5.0 + - - +
688A ASN* 5.3 0.8 + - - -
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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