Contacts of the helix formed by residues 637 - 649 (chain A) in PDB entry 6O0U
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 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A ARG* 2.6 47.9 + - - -
628A LYS* 3.6 28.7 - - + +
629A CYS* 3.6 1.4 - - - -
632A ASP* 3.0 15.9 + - - +
635A CYS 4.5 0.2 - - - +
636A LYS* 1.3 79.6 - - - +
638A TRP* 1.3 61.3 + - - +
639A VAL 3.4 12.1 + - - -
640A HIS* 3.3 11.9 + - + +
641A LYS* 2.9 27.6 + - - +
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Residues in contact with TRP 638 (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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569A ARG* 5.3 0.2 - - - +
603A PHE* 3.6 36.0 - + - -
604A GLU* 3.5 44.0 - - + -
607A LEU* 3.8 29.6 - - + -
608A ILE* 4.2 11.9 - - + -
636A LYS 3.7 7.9 + - - -
637A ASP* 1.3 74.6 + - - +
639A VAL* 1.3 62.0 + - + +
641A LYS* 3.6 33.6 - - + +
642A GLU* 2.9 47.7 + - + +
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Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A SER* 3.8 14.1 - - - +
568A TYR 3.2 32.8 - - - +
569A ARG* 3.5 35.2 - - - +
619A LEU* 4.1 8.3 - - + -
625A ALA* 4.6 3.4 - - + +
626A LEU* 4.5 6.5 - - + -
629A CYS* 4.1 4.3 - - - -
637A ASP* 3.4 1.8 + - - -
638A TRP* 1.3 77.9 - - + +
640A HIS* 1.3 57.9 + - - +
642A GLU* 3.3 8.9 + - - +
643A ILE* 2.9 52.4 + - + +
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Residues in contact with HIS 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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629A CYS* 3.7 19.6 + - + -
632A ASP* 3.0 42.2 + - - +
633A HIS* 5.4 0.4 - - - -
635A CYS* 3.9 12.1 - - + -
637A ASP* 3.3 16.0 + - + +
638A TRP 3.2 0.2 - - - -
639A VAL* 1.3 77.1 - - - +
641A LYS* 1.3 65.6 + - - +
643A ILE* 3.3 1.7 + - - +
644A VAL* 2.9 30.4 + - + +
669A PRO* 3.5 18.4 - - + +
671A ASP* 2.7 35.1 + - - -
672A MET* 3.4 22.7 - - - -
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Residues in contact with LYS 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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604A GLU* 4.0 20.1 + - - -
608A ILE* 5.0 7.4 - - + -
634A ASP 4.7 1.8 + - - -
635A CYS* 2.3 52.1 + - - +
636A LYS* 3.6 13.4 + - - +
637A ASP 2.9 14.9 + - - +
638A TRP* 3.3 42.6 + - + +
640A HIS* 1.3 75.2 - - - +
642A GLU* 1.3 54.9 + - - +
644A VAL* 3.3 2.4 + - - +
645A THR* 2.7 38.4 + - - +
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Residues in contact with GLU 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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565A PHE* 3.6 19.3 - - - -
567A SER* 2.5 38.7 + - - +
568A TYR 4.6 0.7 + - - +
594A ASP* 5.5 2.4 - - - +
607A LEU* 4.0 21.4 - - + +
608A ILE* 5.7 2.0 - - + -
611A VAL* 3.9 16.7 - - + +
617A PHE* 3.7 13.0 - - + -
638A TRP* 2.9 34.4 + - + +
639A VAL* 3.8 6.9 - - - +
640A HIS 3.2 0.2 - - - -
641A LYS* 1.3 77.0 - - - +
643A ILE* 1.3 57.8 + - - +
645A THR* 3.3 6.9 + - - -
646A ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 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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617A PHE* 3.9 17.5 - - + -
619A LEU* 3.6 33.2 - - + -
626A LEU* 4.0 4.5 - - + -
639A VAL* 2.9 36.3 + - + +
640A HIS 3.8 3.6 - - - +
642A GLU* 1.3 74.8 - - - +
644A VAL* 1.3 57.7 + - - +
646A ALA* 3.3 1.9 + - - +
647A LEU* 2.9 34.4 + - + +
653A ILE* 4.9 1.1 - - + +
672A MET* 3.6 44.4 - - + -
675A VAL* 3.9 22.7 - - + -
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Residues in contact with VAL 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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635A CYS* 4.4 7.9 - - - -
640A HIS* 2.9 42.4 + - + +
641A LYS* 3.8 5.6 - - - +
643A ILE* 1.3 75.1 - - - +
645A THR* 1.3 58.9 + - - +
647A LEU* 3.4 3.8 + - - +
648A SER* 2.9 40.5 + - - +
671A ASP* 3.5 47.1 - - + +
672A MET* 4.3 0.9 - - + -
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Residues in contact with THR 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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608A ILE* 3.5 24.2 - - + +
611A VAL* 3.9 17.0 - - + -
612A MET* 3.8 39.7 - - + -
641A LYS 2.7 21.7 + - - -
642A GLU* 3.7 5.6 - - - -
644A VAL* 1.3 78.4 - - - +
646A ALA* 1.3 62.0 + - - +
648A SER* 3.3 6.3 + - - -
649A CYS* 3.0 29.7 + - - -
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Residues in contact with ALA 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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611A VAL* 3.8 4.4 - - + +
617A PHE* 3.5 43.3 - - + -
642A GLU 2.9 17.4 + - - +
643A ILE 3.7 3.6 - - - +
645A THR* 1.3 77.9 - - - +
647A LEU* 1.3 62.6 + - - +
649A CYS 3.4 1.6 + - - -
650A GLY 3.3 3.3 + - - -
651A LYS* 3.0 40.2 + - + +
653A ILE* 4.3 6.7 - - + -
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Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ILE* 2.9 26.6 + - + +
644A VAL* 3.6 4.5 - - - +
646A ALA* 1.3 77.0 - - - +
648A SER* 1.3 60.9 + - - +
650A GLY* 3.1 13.2 + - - -
651A LYS 5.1 0.2 - - - +
653A ILE* 3.6 24.0 - - + -
671A ASP 3.3 26.5 - - - +
672A MET* 3.6 17.3 - - - +
674A ALA* 3.7 29.2 - - + -
675A VAL 4.3 3.1 - - - +
678A PHE* 3.9 13.2 - - + -
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Residues in contact with SER 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A MET* 6.3 1.6 - - - -
644A VAL* 2.9 29.1 + - - +
645A THR* 3.3 8.4 + - - -
647A LEU* 1.3 78.2 - - - +
649A CYS* 1.3 61.1 + - - +
650A GLY 3.1 4.0 + - - -
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Residues in contact with CYS 649 (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 VAL 5.3 0.4 - - - -
612A MET* 3.6 43.7 - - - +
615A ARG* 5.6 0.2 + - - -
645A THR* 3.0 23.7 + - - +
647A LEU 3.3 0.4 - - - -
648A SER* 1.3 77.2 - - - +
650A GLY* 1.3 64.7 + - - +
651A LYS* 3.2 30.4 + - + +
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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