Contacts of the helix formed by residues 647 - 657 (chain A) in PDB entry 2ZT6
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 GLU 647 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644A GLU* 2.9 34.4 + - - +
646A SER* 1.3 82.1 + - - +
648A LEU* 1.3 65.3 + - - +
649A PRO* 3.1 4.8 - - - -
650A SER* 2.8 28.2 + - - +
651A ILE* 3.3 15.9 + - + +
669A TYR* 4.0 23.1 + - + +
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Residues in contact with LEU 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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580A LEU* 4.6 5.4 - - + -
616A VAL* 3.5 21.8 - - + -
630A ALA* 3.4 36.8 - - + -
631A THR 5.0 0.4 - - - -
632A LEU* 3.7 39.9 - - + +
641A ILE* 5.2 0.2 - - + -
643A ALA* 4.0 24.2 - - + +
644A GLU 3.4 8.5 + - - +
645A ILE* 3.9 13.7 - - + +
647A GLU* 1.3 77.2 - - - +
649A PRO* 1.3 68.2 - - + +
651A ILE* 3.0 8.9 + - + +
652A VAL* 2.8 29.1 + - - +
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Residues in contact with PRO 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A LEU* 3.7 15.5 - - + -
583A ALA* 3.7 26.0 - - + -
584A LEU* 3.8 20.7 - - + +
587A HIS* 3.4 27.9 - - + +
589A VAL* 4.9 0.5 - - - +
645A ILE 3.6 5.4 - - - +
646A SER* 3.2 22.2 - - - +
647A GLU 3.2 0.4 - - - -
648A LEU* 1.3 95.1 - - + +
650A SER* 1.3 63.8 + - - +
652A VAL* 3.1 2.8 + - - +
653A GLN* 3.0 22.5 + - - +
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Residues in contact with SER 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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587A HIS* 3.8 21.1 + - - -
646A SER 5.2 0.2 + - - -
647A GLU* 2.8 24.5 + - - +
649A PRO* 1.3 79.2 - - - +
651A ILE* 1.3 63.3 + - - +
653A GLN* 3.5 11.2 + - - +
654A ASP* 3.0 31.8 + - - +
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Residues in contact with ILE 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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632A LEU* 3.6 23.8 - - + -
643A ALA* 4.1 11.4 - - + -
647A GLU* 3.3 19.7 - - + +
648A LEU* 3.0 19.4 + - + +
650A SER* 1.3 77.4 - - - +
652A VAL* 1.3 67.1 - - - +
653A GLN 3.2 0.2 + - - -
654A ASP* 3.2 8.0 + - - +
655A LEU* 3.0 28.7 + - + +
660A ILE* 5.5 1.2 - - + +
665A VAL* 4.3 15.3 - - + -
669A TYR* 3.4 44.9 - - + +
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Residues in contact with VAL 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A CYS* 4.1 12.3 - - + -
584A LEU* 4.5 11.0 - - + -
589A VAL* 4.1 21.8 - - + -
614A PHE* 3.8 23.6 - - + -
616A VAL* 4.5 12.1 - - + -
632A LEU* 3.9 27.8 - - + -
648A LEU* 2.8 29.0 + - - +
649A PRO 3.7 3.6 - - - +
651A ILE* 1.3 72.5 - - - +
653A GLN* 1.3 61.5 + - - +
655A LEU* 3.7 8.5 - - - +
656A ALA* 3.0 23.3 + - + +
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Residues in contact with GLN 653 (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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587A HIS* 2.7 57.0 + - + +
589A VAL* 4.1 14.8 - - + +
649A PRO 3.0 12.0 + - - +
650A SER* 3.5 12.6 - - - +
651A ILE 3.1 0.2 - - - -
652A VAL* 1.3 77.1 - - - +
654A ASP* 1.3 66.9 + - - +
656A ALA* 3.3 2.3 + - - -
657A ASN* 2.9 53.6 + - - +
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Residues in contact with ASP 654 (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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650A SER* 3.0 19.8 + - - +
651A ILE* 3.2 6.9 + - - +
653A GLN* 1.3 85.1 - - - +
655A LEU* 1.3 63.1 + - - +
658A GLY 2.9 4.5 + - - -
659A ASN* 2.7 47.3 + - + +
660A ILE* 3.3 36.8 + - + +
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Residues in contact with LEU 655 (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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555A ALA* 5.1 0.7 - - - +
614A PHE* 3.5 30.2 - - + -
632A LEU* 3.8 29.2 - - + -
651A ILE* 3.0 19.2 + - + +
652A VAL* 3.7 7.9 - - - +
654A ASP* 1.3 78.7 - - - +
656A ALA* 1.3 61.5 + - - +
658A GLY* 3.5 9.0 + - - -
660A ILE* 3.4 25.9 - - + +
661A THR 3.8 9.2 - - - -
662A TRP* 3.8 20.0 - - + +
665A VAL* 3.6 30.3 - - + -
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Residues in contact with ALA 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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555A ALA* 3.2 28.0 - - + +
556A VAL* 5.0 7.1 - - - +
561A LYS* 3.4 34.5 - - + -
589A VAL* 5.4 1.3 - - + -
614A PHE* 3.9 10.3 - - + -
652A VAL* 3.0 18.6 + - + +
653A GLN* 3.8 4.0 - - - +
655A LEU* 1.3 76.2 - - - +
657A ASN* 1.3 64.5 + - - +
658A GLY* 3.1 4.7 + - - -
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Residues in contact with ASN 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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556A VAL* 6.3 1.7 - - - +
561A LYS* 4.6 9.9 - - - +
588A GLY 5.9 1.2 + - - -
589A VAL* 6.2 1.2 - - - +
653A GLN* 2.9 39.3 + - - +
654A ASP 4.1 0.4 - - - +
656A ALA* 1.3 84.4 - - - +
658A GLY* 1.3 62.3 + - - +
659A ASN* 3.3 24.6 + - - +
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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