Contacts of the helix formed by residues 610 - 623 (chain B) in PDB entry 4Z4Q
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 610 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608B ILE* 4.1 3.1 - - - -
609B GLU* 1.3 80.7 - - + +
611B LEU* 1.3 65.3 + - - +
612B ALA* 3.0 5.3 + - + +
613B ARG* 3.2 23.6 + - + +
614B ALA* 3.0 21.5 + - - +
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Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B TYR* 3.7 28.0 - - + +
608B ILE* 3.9 22.9 - - + +
609B GLU 4.2 0.2 - - - -
610B ASP* 1.3 70.9 - - - +
612B ALA* 1.3 66.5 + - - +
614B ALA* 3.5 1.3 + - - +
615B GLU* 3.2 20.3 + - + +
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Residues in contact with ALA 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ASP* 3.0 3.2 + - + -
611B LEU* 1.3 77.8 - - - +
613B ARG* 1.3 61.6 + - + +
614B ALA 2.9 10.0 + - - -
615B GLU* 2.9 16.6 + - - +
616B ARG* 3.5 10.6 + - - +
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Residues in contact with ARG 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ASP* 3.2 21.0 + - + +
612B ALA* 1.3 80.3 - - + +
614B ALA* 1.3 58.2 + - - +
616B ARG* 4.2 5.9 + - - +
617B ARG* 3.5 24.1 + - - +
1010B GLU* 4.2 11.1 - - + +
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Residues in contact with ALA 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B TYR* 4.1 9.2 + - + -
608B ILE* 4.6 8.7 - - + -
610B ASP 3.0 17.6 + - - +
611B LEU* 3.9 6.7 - - - +
612B ALA 2.9 1.2 + - - -
613B ARG* 1.3 76.8 - - - +
615B GLU* 1.3 62.9 + - - +
617B ARG* 3.9 5.2 - - - +
618B VAL* 3.3 28.2 + - - +
1009B LEU* 4.3 20.0 - - + -
1010B GLU* 4.4 15.9 - - + +
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Residues in contact with GLU 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523B TYR* 2.8 36.0 + - - +
524B ARG* 5.8 3.5 + - - -
611B LEU* 3.2 14.0 + - + +
612B ALA* 2.9 10.7 + - - +
614B ALA* 1.3 74.3 - - - +
616B ARG* 1.3 65.5 + - - +
618B VAL* 3.3 2.9 + - - +
619B ASN* 3.0 53.2 + - - +
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Residues in contact with ARG 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B ALA 3.5 9.1 + - - +
613B ARG* 4.6 4.9 - - - +
615B GLU* 1.3 78.8 - - - +
617B ARG* 1.3 63.7 + - - +
619B ASN* 4.1 5.1 - - - +
620B VAL* 2.9 28.1 + - - +
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Residues in contact with ARG 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613B ARG* 3.5 22.5 + - - +
614B ALA 3.9 5.2 - - - +
615B GLU 3.2 0.6 - - - -
616B ARG* 1.3 80.7 - - - +
618B VAL* 1.3 62.0 + - + +
620B VAL* 4.0 2.4 - - - +
621B LEU* 3.3 47.9 + - + +
632B TRP* 3.8 30.9 - - - +
636B ASN* 5.6 0.8 - - - +
1010B GLU* 3.1 48.1 + - - +
1011B ASP* 4.6 3.0 - - - +
1013B MET* 4.4 6.1 - - + -
1014B GLY* 3.3 17.1 - - - +
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Residues in contact with VAL 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ALA* 5.3 3.1 - - + +
520B THR* 3.9 27.1 - - - +
523B TYR* 4.7 19.3 - - + -
524B ARG* 5.1 7.4 - - - -
614B ALA 3.3 18.5 + - - +
615B GLU 4.0 2.9 - - - +
617B ARG* 1.3 78.0 - - + +
619B ASN* 1.3 64.0 + - - +
622B MET* 3.0 32.5 + - + +
1009B LEU* 4.1 22.9 - - + -
1013B MET* 3.7 26.7 - - + -
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Residues in contact with ASN 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ALA* 5.7 3.3 - - - +
523B TYR* 6.0 0.3 - - - -
524B ARG* 5.0 10.0 + - - -
615B GLU* 3.0 48.9 + - - +
616B ARG* 4.1 4.6 - - - +
618B VAL* 1.3 82.2 - - - +
620B VAL* 1.3 68.4 + - - +
623B GLY* 3.0 25.5 + - - +
625B LYS 5.5 0.5 - - - +
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Residues in contact with VAL 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B ARG 2.9 18.0 + - - +
617B ARG* 4.0 3.4 - - - +
619B ASN* 1.3 79.3 - - - +
621B LEU* 1.3 63.1 + - + +
622B MET 3.5 0.2 + - - -
625B LYS 4.6 2.8 - - - +
628B PRO* 4.9 17.0 - - + +
629B ARG* 3.6 27.0 + - - +
632B TRP* 4.5 27.1 - - + -
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B LYS* 4.7 2.1 + - - -
617B ARG* 3.3 35.0 + - - +
619B ASN 3.3 0.2 - - - -
620B VAL* 1.3 78.4 - - + +
622B MET* 1.3 73.5 + - + +
629B ARG* 3.0 26.6 + - + +
632B TRP* 3.5 48.0 - - + -
1013B MET* 3.7 37.5 - - + +
1014B GLY* 4.3 1.1 - - - +
1017B PHE* 3.8 31.5 - - + -
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Residues in contact with MET 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B ASN* 3.2 33.5 + - - +
463B ALA* 3.2 24.2 - - + +
464B LYS* 3.6 3.8 - - - +
513B HIS* 5.1 1.8 - - - +
516B THR* 2.8 38.8 - - + -
517B LEU* 3.6 25.4 - - + -
520B THR* 3.6 15.9 - - + -
618B VAL* 3.0 16.7 + - + +
621B LEU* 1.3 86.1 - - + +
623B GLY* 1.3 65.1 + - - +
629B ARG* 4.0 0.7 - - - -
1013B MET* 3.5 22.4 - - + -
1017B PHE* 4.0 14.8 - - + -
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Residues in contact with GLY 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ALA* 3.5 11.2 - - - -
464B LYS* 3.2 8.2 - - - -
618B VAL 4.1 0.4 + - - -
619B ASN* 3.0 24.7 + - - +
621B LEU 3.6 0.8 - - - -
622B MET* 1.3 77.3 - - - +
624B ASP* 1.3 61.1 + - - -
625B LYS 3.3 3.4 - - - -
629B ARG* 2.3 32.6 + - - +
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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