Contacts of the helix formed by residues 634 - 651 (chain A) in PDB entry 4MS0
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 634 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ASN* 3.9 10.5 + - - -
589A SER* 2.6 36.0 + - - +
592A GLU* 3.8 23.8 - - - +
631A ILE 3.1 16.1 + - - +
632A ALA 3.5 9.3 - - - +
633A THR* 1.3 75.4 + - - +
635A LEU* 1.3 59.8 + - - +
636A ALA* 3.2 28.2 + - - +
637A LEU* 2.9 25.7 + - + +
638A TYR 3.6 1.4 + - - -
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A THR 3.3 10.1 + - - +
634A ASP* 1.3 69.0 + - - +
636A ALA* 1.3 67.0 + - - +
638A TYR* 3.0 29.9 + - + +
639A PHE* 3.2 25.0 - - + -
671A THR* 4.2 13.9 - - + -
674A ASP* 5.5 3.8 - - - +
675A LEU* 4.3 16.4 - - + -
729A PHE* 4.2 24.9 - - + -
733A VAL* 4.0 23.8 - - + -
900A 2ZX 5.1 5.6 - - + +
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Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ASP* 3.1 21.9 + - - +
635A LEU* 1.3 79.3 - - - +
637A LEU* 1.3 63.6 + - + +
638A TYR 3.6 0.2 + - - -
639A PHE* 3.9 17.8 + - - +
640A GLY 4.8 1.6 + - - -
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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
----------------------------------------------------------
588A THR* 6.6 0.4 - - - -
589A SER* 3.6 19.1 - - - +
631A ILE* 3.5 38.8 - - + +
632A ALA* 4.7 7.9 - - - +
634A ASP* 2.9 15.7 + - + +
636A ALA* 1.3 79.1 - - + +
638A TYR* 1.3 66.0 + - - +
639A PHE 3.3 1.1 + - - -
640A GLY* 3.5 3.4 + - - -
641A ASN* 3.0 24.3 + - + +
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Residues in contact with TYR 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ALA 5.1 3.1 - - - +
634A ASP 3.6 3.2 + - - +
635A LEU* 3.0 23.2 + - + +
637A LEU* 1.3 78.3 - - - +
639A PHE* 1.3 91.6 + + - +
641A ASN* 3.2 6.4 + - + +
642A ARG* 2.8 55.0 + - + +
668A LEU* 3.8 9.9 - - + -
671A THR* 3.7 32.3 - - + +
732A ALA 4.2 1.1 + - - -
733A VAL* 3.1 38.9 + - + -
736A PRO* 3.6 13.0 - - - +
737A CYS* 3.2 29.2 + - + -
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Residues in contact with PHE 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A LEU* 3.2 34.8 - - + -
636A ALA* 3.9 11.9 - - - +
637A LEU 3.3 0.6 - - - -
638A TYR* 1.3 96.6 - + - +
640A GLY* 1.3 63.3 + - - +
642A ARG* 3.9 2.5 - - - +
643A LYS* 3.1 25.1 + - - +
732A ALA* 3.7 26.2 - - + -
733A VAL* 3.9 20.0 - - + -
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Residues in contact with GLY 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ALA 4.8 1.8 + - - -
637A LEU 3.5 5.1 + - - -
638A TYR 3.4 0.2 - - - -
639A PHE* 1.3 76.2 - - - +
641A ASN* 1.3 64.6 + - - +
643A LYS* 3.8 8.2 - - - +
644A GLN* 3.0 29.2 + - - +
664A ARG* 4.5 2.9 - - - -
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Residues in contact with ASN 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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632A ALA* 6.0 0.4 - - - +
637A LEU* 3.0 20.2 + - + +
638A TYR* 3.6 7.5 - - - +
640A GLY* 1.3 74.6 - - - +
642A ARG* 1.3 57.8 + - - +
644A GLN* 3.3 2.6 + - - +
645A LEU* 3.0 36.1 + - - +
664A ARG* 3.0 69.2 + - - +
667A GLY* 3.9 6.2 - - - -
668A LEU* 3.4 19.4 - - - +
671A THR* 5.6 0.8 + - - -
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Residues in contact with ARG 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A TYR* 2.8 54.0 + - + +
639A PHE 3.9 2.9 - - - +
641A ASN* 1.3 73.3 - - - +
643A LYS* 1.3 62.6 + - - +
645A LEU* 3.3 6.3 + - - +
646A GLU* 2.8 58.0 + - - +
668A LEU* 4.3 10.3 - - + -
736A PRO* 3.4 34.1 + - - +
739A THR* 4.6 10.5 - - - +
740A THR* 2.8 32.5 + - - +
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Residues in contact with LYS 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 PHE 3.1 18.8 + - - +
640A GLY* 3.8 8.3 - - - +
641A ASN 3.3 0.2 - - - -
642A ARG* 1.3 84.2 - - - +
644A GLN* 1.3 64.3 + - - +
646A GLU* 3.4 5.5 + - - +
647A GLU* 3.0 24.5 + - + +
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Residues in contact with GLN 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 GLY 3.0 19.2 + - - +
641A ASN 3.5 4.5 - - - +
643A LYS* 1.3 77.7 - - - +
645A LEU* 1.3 57.1 + - - +
647A GLU* 3.1 12.7 + - - +
648A MET* 2.8 55.4 + - + +
664A ARG* 3.7 35.3 + - - +
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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
----------------------------------------------------------
641A ASN* 3.0 29.7 + - - +
642A ARG* 3.7 3.8 - - - +
644A GLN* 1.3 76.2 - - - +
646A GLU* 1.3 57.5 + - - +
648A MET* 3.2 9.4 + - - +
649A TYR* 2.8 31.0 + - - +
654A LEU* 4.1 18.5 - - + +
664A ARG* 3.3 45.3 - - + +
665A VAL* 3.9 22.9 - - + +
668A LEU* 3.8 23.6 - - + -
740A THR* 4.1 13.2 - - + -
744A ILE* 4.2 8.8 - - + +
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Residues in contact with GLU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ARG* 2.8 42.9 + - - +
643A LYS* 3.7 6.3 - - - +
645A LEU* 1.3 77.7 - - - +
647A GLU* 1.3 57.2 + - - +
649A TYR* 3.3 4.5 + - - +
650A GLN* 2.9 41.2 + - + +
740A THR* 3.0 26.3 + - - +
743A GLN* 3.0 28.6 + - - +
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Residues in contact with GLU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LYS* 3.0 14.5 + - + +
644A GLN* 3.3 17.3 - - - +
646A GLU* 1.3 78.0 - - - +
648A MET* 1.3 59.4 + - + +
650A GLN* 3.4 4.7 + - - +
651A THR* 3.0 36.7 + - + +
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Residues in contact with MET 648 (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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644A GLN* 2.8 47.7 + - - +
645A LEU* 3.2 9.2 + - - +
647A GLU* 1.3 71.8 - - + +
649A TYR* 1.3 60.8 + - - +
651A THR* 3.3 0.6 + - - -
652A GLY 3.2 2.1 + - - -
653A SER* 2.9 46.7 + - - +
654A LEU* 3.1 23.4 + - + +
660A SER* 5.7 0.7 - - - +
661A HIS* 3.5 39.5 - - + +
664A ARG* 4.3 22.2 - - - +
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Residues in contact with TYR 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LEU 2.8 20.5 + - - +
646A GLU* 3.6 9.0 - - - +
648A MET* 1.3 72.6 - - - +
650A GLN* 1.3 65.7 + - + +
652A GLY* 3.2 13.2 + - - -
654A LEU* 4.2 13.1 - - + +
740A THR* 5.7 0.2 - - + -
743A GLN* 3.3 66.8 + - + +
744A ILE* 4.7 15.3 - - + -
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Residues in contact with GLN 650 (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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646A GLU* 2.9 27.8 + - + +
647A GLU* 3.9 4.5 - - - +
649A TYR* 1.3 83.1 - - + +
651A THR* 1.3 61.8 + - + +
652A GLY 3.3 0.2 - - - -
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Residues in contact with THR 651 (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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647A GLU* 3.0 21.3 + - + +
648A MET* 3.3 5.9 + - - -
650A GLN* 1.3 79.3 - - + +
652A GLY* 1.3 61.7 + - - +
653A SER* 3.4 16.9 + - - -
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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
------------------------------------------------------------
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