Contacts of the helix formed by residues 655 - 667 (chain A) in PDB entry 5A31
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 SER 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A TYR 4.3 0.2 + - - -
654A HIS* 1.3 78.6 - - - +
656A GLU* 1.3 67.0 + - - +
657A TRP* 3.3 7.0 + - - +
658A ASN* 3.1 28.2 + - - +
659A LEU* 3.4 21.3 + - - +
744O LEU* 5.5 2.2 - - - -
745O PRO 5.1 10.3 + - - -
746O SER* 5.7 5.8 - - - -
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Residues in contact with GLU 656 (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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613A ALA 2.4 30.5 - - - +
614A THR* 3.8 10.5 - - + -
615A SER* 3.2 32.2 + - - +
618A VAL* 4.0 9.9 - - + +
641A TRP* 4.5 6.9 - - - -
645A HIS* 2.9 31.4 + - - +
655A SER* 1.3 76.8 - - - +
657A TRP* 1.3 67.7 + - - +
659A LEU* 3.5 9.4 - - + +
660A PHE* 3.0 24.0 + - - +
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Residues in contact with TRP 657 (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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615A SER* 6.2 0.7 - - - -
617A LEU* 3.8 34.8 - - + -
618A VAL* 3.8 25.4 - - + -
621A CYS* 3.9 26.2 - - - -
655A SER* 3.3 5.4 + - - +
656A GLU* 1.3 81.8 - - - +
658A ASN* 1.3 67.2 + - + +
660A PHE* 3.2 14.2 + + - +
661A VAL* 2.9 53.8 + - + +
766A LEU* 5.5 0.2 - - + -
785A SER* 2.7 32.3 + - - +
786A LEU* 3.8 26.7 - - + -
789A LEU* 3.7 22.4 - - + +
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Residues in contact with ASN 658 (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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654A HIS* 5.0 14.8 + - + +
655A SER* 3.1 24.6 + - - +
657A TRP* 1.3 84.4 - - + +
659A LEU* 1.3 62.5 + - - +
661A VAL* 3.4 5.8 + - - +
662A THR* 3.1 29.7 + - - +
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Residues in contact with LEU 659 (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 TRP* 3.8 20.2 - - + +
644A VAL* 4.2 30.7 - - + +
645A HIS* 4.5 12.3 - - - +
647A ALA* 4.9 12.6 - - + -
654A HIS* 4.6 20.1 - - + +
655A SER 3.4 14.9 + - - +
656A GLU* 3.3 15.0 + - + +
657A TRP 3.2 0.2 - - - -
658A ASN* 1.3 75.4 - - - +
660A PHE* 1.3 71.7 + - - +
662A THR* 2.9 27.1 + - - +
663A CYS* 3.1 8.7 + - - +
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Residues in contact with PHE 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A VAL* 3.7 22.7 - - + -
621A CYS* 4.4 9.2 - - + -
622A LEU* 3.6 27.8 - - + -
625A ILE* 4.0 16.4 - - + -
637A MET* 5.6 3.8 - - - -
641A TRP* 3.6 34.1 - + + +
656A GLU 3.0 17.0 + - - +
657A TRP* 3.5 28.7 - + - +
659A LEU* 1.3 78.2 - - - +
661A VAL* 1.3 69.4 + - + +
663A CYS* 3.2 5.7 + - - +
664A LEU* 3.0 60.7 + - + +
766A LEU* 5.6 0.2 - - + -
789A LEU* 4.8 0.9 - - + -
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Residues in contact with VAL 661 (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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657A TRP* 2.9 61.1 + - + +
658A ASN* 3.8 8.3 - - - +
660A PHE* 1.3 80.8 - - + +
662A THR* 1.3 62.3 + - + +
664A LEU* 3.5 3.6 + - + +
665A MET* 2.9 36.9 + - + +
788A GLU* 5.9 6.1 - - + +
789A LEU* 4.0 25.6 - - + -
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Residues in contact with THR 662 (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 VAL* 6.1 0.2 - - - +
658A ASN* 3.1 28.6 + - - +
659A LEU* 2.9 19.7 + - - +
661A VAL* 1.3 78.9 - - + +
663A CYS* 1.3 54.6 + - - +
665A MET* 3.4 5.5 + - - +
666A ASN* 2.6 37.1 + - - -
670A TYR* 5.5 0.5 - - - +
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Residues in contact with CYS 663 (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 MET* 5.5 6.3 - - - -
640A LYS* 4.0 30.7 - - - -
641A TRP* 4.0 31.4 - - + -
644A VAL* 5.3 11.0 - - + -
659A LEU 3.1 7.9 + - - +
660A PHE 3.2 9.2 + - - +
662A THR* 1.3 82.0 + - - +
664A LEU* 1.3 63.4 + - - +
666A ASN* 3.1 26.9 + - - +
667A MET* 3.6 9.7 + - - +
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Residues in contact with LEU 664 (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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625A ILE* 4.4 6.1 - - + -
637A MET* 5.2 11.4 - - + -
660A PHE* 3.0 49.8 + - + +
661A VAL* 4.3 2.9 - - + +
663A CYS* 1.3 78.7 - - - +
665A MET* 1.3 62.3 + - + +
667A MET* 3.4 23.6 + - + +
668A MET* 3.4 27.6 - - + +
762A ILE* 4.4 22.4 - - + -
766A LEU* 4.2 20.0 - - + -
789A LEU* 4.3 16.6 - - + -
793A LEU* 6.1 0.7 - - + -
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Residues in contact with MET 665 (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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661A VAL* 2.9 26.5 + - + +
662A THR* 3.4 6.0 + - - +
664A LEU* 1.3 75.5 - - + +
666A ASN* 1.3 54.4 + - - +
668A MET* 2.9 37.1 + - + +
669A GLY 2.5 65.7 + - - +
670A TYR* 4.9 6.1 - - + -
789A LEU* 6.2 4.5 - - + -
792A GLN* 5.8 15.9 - - + +
793A LEU* 5.5 9.9 - - - -
796A ASP* 6.1 4.9 - - + +
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Residues in contact with ASN 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A THR* 2.6 31.7 + - - -
663A CYS* 3.1 14.8 + - - +
665A MET* 1.3 72.3 - - - +
667A MET* 1.3 64.5 + - + +
668A MET 2.8 11.5 + - - -
669A GLY* 3.4 13.0 + - - +
670A TYR* 4.5 13.5 - - - +
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Residues in contact with MET 667 (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 MET* 3.9 28.0 - - + -
640A LYS* 4.6 23.6 - - + -
663A CYS* 3.8 12.6 - - - +
664A LEU* 3.4 15.4 + - + +
666A ASN* 1.3 77.6 - - + +
668A MET* 1.3 62.3 + - + +
757A THR* 3.9 25.8 + - - +
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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