Contacts of the helix formed by residues 637 - 649 (chain A) in PDB entry 1Y8B
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 ILE 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A GLU* 5.1 10.5 - - - +
458A GLY* 5.4 9.9 - - - -
509A TRP* 3.4 43.1 - - + -
510A ALA 5.3 1.1 - - - +
511A MET* 6.0 2.5 - - + -
534A TRP* 5.9 4.5 - - + -
633A ALA 4.1 9.6 - - - +
634A THR 3.2 0.2 + - - -
635A LEU 3.0 1.6 - - - -
636A ARG* 1.3 84.7 - - + +
638A SER* 1.3 69.2 + - - +
639A SER 3.5 0.7 - - - -
640A GLN* 3.7 27.8 - - - +
641A HIS* 2.7 42.7 + - + +
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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
----------------------------------------------------------
511A MET* 4.3 24.5 + - - +
599A ASN* 4.1 27.2 + - - +
602A GLY* 6.0 0.2 - - - -
633A ALA 4.6 1.1 - - - -
634A THR* 2.6 41.1 + - - +
637A ILE* 1.3 81.2 - - - +
639A SER* 1.3 60.3 + - - -
641A HIS* 3.2 11.5 + - - +
642A ILE* 3.2 15.8 + - - +
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Residues in contact with SER 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 2.9 31.7 - - - +
634A THR* 3.1 4.2 + - - +
635A LEU* 3.8 30.4 - - - +
638A SER* 1.3 79.3 - - - +
640A GLN* 1.3 63.6 + - - +
642A ILE* 3.2 27.3 + - - +
643A ALA 3.7 2.8 + - - -
696A LEU* 5.1 9.5 + - - +
697A ILE* 5.7 0.2 - - - +
708A THR* 3.8 15.7 + - - +
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Residues in contact with GLN 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLY* 5.4 9.5 + - - -
635A LEU 4.1 6.3 + - - +
636A ARG 4.6 6.1 + - - +
637A ILE* 3.4 34.2 + - - +
638A SER 3.2 0.4 - - - -
639A SER* 1.3 79.5 - - - +
641A HIS* 1.3 63.0 + - - +
643A ALA* 3.4 18.3 + - + +
644A ASN* 3.7 10.7 + - - +
703A GLN* 5.3 0.7 - - - +
706A GLY 4.0 14.8 - - - +
707A TYR* 3.5 32.9 - - - +
708A THR* 3.3 25.3 + - + +
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Residues in contact with HIS 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A MET* 6.3 1.3 - - + -
465A MET* 4.1 18.6 - - + -
509A TRP* 6.3 4.2 - + - -
583A GLU* 4.6 7.3 + - + -
599A ASN* 6.5 0.4 - - - -
637A ILE* 2.7 30.9 + - + +
638A SER* 3.2 6.3 + - - +
640A GLN* 1.3 72.7 - - - +
642A ILE* 1.3 68.5 + - - +
644A ASN* 2.9 26.9 + - - +
645A TRP* 2.5 69.1 + + + -
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Residues in contact with ILE 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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599A ASN* 3.7 34.3 - - + +
600A VAL* 4.3 11.7 - - + +
603A ILE* 3.6 30.7 - - + -
638A SER 3.2 9.2 + - - +
639A SER* 3.2 14.8 + - - +
641A HIS* 1.3 78.6 - - - +
643A ALA* 1.3 56.6 - - - +
645A TRP* 2.9 10.8 + - - -
646A LEU* 2.5 63.9 + - + +
697A ILE* 4.6 16.6 - - + +
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Residues in contact with ALA 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 SER 3.7 3.8 + - - +
640A GLN* 3.4 13.3 + - + +
641A HIS 3.1 0.2 - - - -
642A ILE* 1.3 79.3 - - - +
644A ASN* 1.3 68.0 + - - +
646A LEU* 4.5 4.9 - - - -
647A ARG* 2.7 28.8 + - - +
700A GLY* 5.2 1.3 - - - +
701A VAL* 4.0 28.2 - - + +
703A GLN* 5.4 4.7 - - - +
708A THR* 5.1 11.2 - - + -
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Residues in contact with ASN 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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462A HIS* 5.4 5.4 + - - -
465A MET* 3.4 41.5 - - + +
640A GLN* 3.7 16.5 + - - +
641A HIS* 2.9 27.9 + - - +
643A ALA* 1.3 78.6 - - - +
645A TRP* 1.3 69.0 + - + +
647A ARG* 3.4 15.8 - - - +
648A HIS* 3.4 8.3 + - - +
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Residues in contact with TRP 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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465A MET* 5.6 0.4 - - + -
583A GLU* 3.3 17.4 + - - -
587A TRP* 3.5 45.8 - + + -
595A GLU* 3.2 36.1 - - + -
599A ASN* 3.6 25.6 - - - -
641A HIS* 2.5 55.7 + + - +
642A ILE* 2.9 11.6 + - + +
644A ASN* 1.3 76.4 - - + +
646A LEU* 1.3 61.5 + - + +
647A ARG 2.6 5.5 + - - -
648A HIS 2.7 3.0 + - - -
649A GLY* 2.3 37.3 + - - -
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Residues in contact with LEU 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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596A LEU* 5.0 12.6 - - + -
642A ILE* 2.5 43.7 + - + +
643A ALA* 4.0 4.3 - - - +
645A TRP* 1.3 79.0 - - + +
647A ARG* 1.3 61.4 + - - +
649A GLY* 3.8 8.6 + - - +
650A ILE 4.5 3.6 + - - -
651A LEU* 3.4 45.1 + - + +
656A VAL* 4.3 15.0 - - + -
697A ILE* 4.8 14.1 - - + +
701A VAL* 6.3 1.1 - - + -
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Residues in contact with ARG 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 3.4 29.9 + - - +
643A ALA 2.7 22.6 + - - +
644A ASN* 3.4 11.7 - - - +
645A TRP 2.6 4.2 + - - -
646A LEU* 1.3 74.7 - - - +
648A HIS* 1.3 58.0 + - + +
649A GLY 3.9 0.2 + - - -
650A ILE* 5.0 1.2 + - - +
701A VAL* 4.0 25.8 - - + +
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Residues in contact with HIS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A GLU* 5.5 9.6 + - + +
585A ALA* 3.4 30.4 - - + +
587A TRP* 5.0 0.4 - - - -
644A ASN 3.4 6.2 + - - +
645A TRP 2.7 8.9 + - - +
647A ARG* 1.3 80.0 + - + +
649A GLY* 1.3 56.1 + - - -
650A ILE* 3.2 23.2 + - + +
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Residues in contact with GLY 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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585A ALA* 5.0 1.1 - - - -
587A TRP* 4.1 18.2 - - - -
592A ILE* 4.2 13.3 - - - +
645A TRP* 2.3 27.9 + - - -
646A LEU* 3.8 3.9 + - - -
647A ARG 3.5 1.4 - - - -
648A HIS* 1.3 68.8 - - - +
650A ILE* 1.3 79.3 + - - +
651A LEU* 3.6 11.6 - - - +
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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