Contacts of the helix formed by residues 643 - 651 (chain A) in PDB entry 5EPG
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 THR 643 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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627A ILE* 4.8 19.0 - - + +
629A LEU* 3.9 22.4 - - + -
642A MET* 1.3 77.8 - - - +
644A ALA* 1.3 66.3 + - - +
645A GLU* 3.2 21.4 + - - +
646A HIS* 3.1 37.1 + - + +
647A LEU* 3.7 3.8 + - - +
663A LEU* 3.7 11.1 - - - +
664A ALA 5.8 0.4 - - - -
675A VAL 4.0 12.6 - - - -
676A CYS* 4.1 9.9 - - - -
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Residues in contact with ALA 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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643A THR* 1.3 78.8 + - - +
645A GLU* 1.3 60.9 + - - +
647A LEU* 3.4 4.5 + - - +
648A SER* 3.2 18.4 + - - +
651A ASN* 4.0 15.7 - - - +
663A LEU* 3.7 20.2 - - + +
664A ALA 3.3 24.8 + - - +
665A THR* 3.8 22.2 - - + +
675A VAL 4.5 0.6 + - - -
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Residues in contact with GLU 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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643A THR* 3.2 15.4 + - - +
644A ALA* 1.3 77.0 - - - +
646A HIS* 1.3 72.2 + - + +
648A SER* 3.3 18.7 + - - +
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Residues in contact with HIS 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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629A LEU* 5.1 3.7 - - + +
640A ASP* 4.7 2.7 - - - -
641A ILE 3.5 17.9 + - - -
642A MET* 3.9 17.7 - - + -
643A THR* 3.1 47.8 + - + +
645A GLU* 1.3 85.6 - - + +
647A LEU* 1.3 60.1 + - - +
648A SER* 3.6 2.0 + - - -
823A PHE* 3.3 21.5 - - - -
827A LYS* 4.4 19.5 + - - +
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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
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642A MET* 4.1 13.2 - - + -
643A THR 3.8 4.3 - - - +
644A ALA 3.4 5.0 + - - +
646A HIS* 1.3 82.9 - - - +
648A SER* 1.3 71.0 + - - +
649A ASP 3.2 0.3 + - - -
650A VAL* 3.0 40.8 + - - +
651A ASN* 3.9 18.6 - - + +
662A PHE* 4.1 17.7 - - + -
663A LEU* 3.7 31.9 - - + -
788A THR* 5.7 1.6 - - + -
820A VAL* 4.2 18.8 - - + -
823A PHE* 4.1 31.6 - - + -
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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
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644A ALA 3.2 11.0 + - - +
645A GLU* 3.3 14.4 + - - +
646A HIS 4.9 1.9 + - - -
647A LEU* 1.3 80.1 + - - +
649A ASP* 1.3 70.7 + - - -
650A VAL* 3.2 3.5 + - - +
651A ASN* 3.5 15.4 - - - +
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Residues in contact with ASP 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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648A SER* 1.3 81.4 + - - +
650A VAL* 1.3 73.9 + - - +
651A ASN 3.5 1.7 + - - -
652A SER* 5.2 4.2 + - - +
790A LYS* 2.8 34.5 + - - -
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Residues in contact with VAL 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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647A LEU* 3.0 24.6 + - - +
648A SER* 5.2 0.4 - - - +
649A ASP* 1.3 91.7 - - - +
651A ASN* 1.3 54.9 + - - +
652A SER 3.4 9.4 - - - +
662A PHE* 3.4 19.9 - - - -
787A SER* 3.5 18.6 - - - +
788A THR* 3.3 35.9 - - - +
790A LYS* 4.2 18.4 - - + +
823A PHE* 4.0 20.0 - - + -
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Residues in contact with ASN 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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644A ALA* 4.0 12.0 - - - +
647A LEU* 3.9 15.3 - - + +
648A SER 3.5 16.7 + - - +
649A ASP 3.5 1.8 - - - -
650A VAL* 1.3 77.1 - - - +
652A SER* 1.3 61.4 + - - +
661A LYS* 3.1 17.5 - - - +
662A PHE* 2.9 23.7 + - - +
663A LEU* 3.2 41.0 + - - +
665A THR* 4.0 16.6 - - - +
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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