Contacts of the helix formed by residues 610 - 623 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A ILE 5.1 0.2 - - - -
609A GLU* 1.3 81.1 - - + +
611A LEU* 1.3 55.3 + - - +
612A ALA* 2.7 24.4 + - - +
613A ARG* 3.1 30.3 + - + +
614A ALA* 2.9 22.9 + - - +
1008A SER* 5.1 1.0 + - - -
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Residues in contact with LEU 611 (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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523A TYR* 3.9 26.5 - - + +
527A ARG* 6.4 1.1 - - + -
608A ILE* 5.1 15.3 + - + -
609A GLU 4.1 1.0 - - - -
610A ASP* 1.3 70.4 + - - +
612A ALA* 1.3 56.6 + - - +
614A ALA* 3.9 4.2 - - + +
615A GLU* 3.3 21.5 + - - +
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Residues in contact with ALA 612 (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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610A ASP* 2.7 12.8 + - - +
611A LEU* 1.3 73.6 - - - +
613A ARG* 1.3 63.0 + - - +
614A ALA 2.9 5.8 + - - -
615A GLU* 3.0 16.7 + - - +
616A ARG* 3.2 12.6 + - - +
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Residues in contact with ARG 613 (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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610A ASP* 3.0 29.9 + - + +
612A ALA* 1.3 75.3 - - - +
614A ALA* 1.3 56.1 + - - +
616A ARG* 3.9 7.0 + - - +
617A ARG* 3.4 24.8 + - - +
1010A GLU* 4.4 11.1 - - + +
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Residues in contact with ALA 614 (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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523A TYR* 4.3 7.2 - - + -
608A ILE* 5.2 7.0 - - + -
609A GLU 5.8 0.4 - - - +
610A ASP 2.9 18.4 + - - +
611A LEU* 3.9 8.5 - - + +
612A ALA 2.9 0.6 - - - -
613A ARG* 1.3 75.8 - - - +
615A GLU* 1.3 64.7 + - - +
616A ARG 3.2 1.3 - - - -
617A ARG* 3.5 4.5 + - - +
618A VAL* 3.2 28.2 + - - +
1008A SER* 6.0 0.7 - - - +
1009A LEU* 4.5 21.1 - - + -
1010A GLU* 4.6 14.6 - - + +
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Residues in contact with GLU 615 (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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523A TYR* 2.7 50.9 + - - +
524A ARG* 5.2 8.4 + - - -
611A LEU 3.3 9.2 + - - +
612A ALA* 3.0 11.0 + - - +
614A ALA* 1.3 78.8 - - - +
616A ARG* 1.3 58.3 + - - +
618A VAL* 3.9 0.7 - - - +
619A ASN* 2.9 38.2 + - + +
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Residues in contact with ARG 616 (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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612A ALA 3.2 13.5 + - - +
613A ARG* 4.1 7.9 - - - +
615A GLU* 1.3 76.6 - - - +
617A ARG* 1.3 60.8 + - - +
619A ASN* 4.6 3.6 - - - -
620A VAL* 2.8 43.2 + - + +
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Residues in contact with ARG 617 (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 ARG 3.4 16.2 + - - +
614A ALA 3.9 4.0 - - - +
615A GLU 3.4 0.4 - - - -
616A ARG* 1.3 78.6 - - - +
618A VAL* 1.3 58.1 + - + +
620A VAL* 3.9 3.5 - - - +
621A LEU* 3.1 44.1 + - + +
632A TRP* 3.2 40.9 - - - +
636A ASN* 4.8 3.0 - - - +
1010A GLU* 3.0 43.0 + - - +
1011A ASP* 5.6 0.8 + - - +
1013A MET* 4.2 11.0 - - + -
1014A GLY* 4.2 12.6 - - - +
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Residues in contact with VAL 618 (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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463A ALA* 5.6 4.5 - - + -
519A LEU 6.2 0.2 - - - -
520A THR* 3.9 28.5 - - + -
523A TYR* 4.1 31.0 - - + -
524A ARG* 5.2 7.2 - - + +
614A ALA 3.2 16.5 + - - +
615A GLU 4.1 2.2 - - - +
617A ARG* 1.3 76.8 - - + +
619A ASN* 1.3 67.7 + - - +
620A VAL 3.2 0.2 + - - -
622A MET* 3.0 26.7 + - + +
1009A LEU* 4.2 16.8 - - + +
1013A MET* 3.6 24.9 - - + -
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Residues in contact with ASN 619 (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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463A ALA* 6.1 2.2 - - - -
615A GLU* 2.9 32.1 + - + +
616A ARG* 3.9 4.7 - - - +
618A VAL* 1.3 77.2 - - - +
620A VAL* 1.3 58.9 + - + +
623A GLY* 3.1 28.9 + - - +
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Residues in contact with VAL 620 (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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616A ARG* 2.8 38.0 + - + +
617A ARG* 3.9 4.7 - - - +
618A VAL 3.1 0.2 - - - -
619A ASN* 1.3 77.9 - - + +
621A LEU* 1.3 62.1 + - + +
622A MET 3.6 0.2 + - - -
625A LYS 4.7 2.4 - - - +
628A PRO* 3.8 34.6 - - + +
629A ARG* 3.8 22.2 + - - +
632A TRP* 4.0 27.8 - - + -
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Residues in contact with LEU 621 (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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464A LYS* 5.6 0.2 - - - -
617A ARG* 3.1 28.6 + - + +
620A VAL* 1.3 79.0 - - + +
622A MET* 1.3 75.5 + - + +
629A ARG* 3.3 20.6 + - + +
632A TRP* 3.5 54.1 - - + +
1013A MET* 3.4 36.6 - - + +
1017A PHE* 3.6 40.1 - - + -
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Residues in contact with MET 622 (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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461A ASN* 3.0 38.6 + - - +
463A ALA* 3.6 11.2 - - + +
464A LYS* 3.2 11.6 - - - +
513A HIS* 5.0 2.2 - - - +
516A THR* 3.0 38.6 - - + +
517A LEU* 3.6 27.4 - - + -
520A THR* 3.3 30.3 - - + -
618A VAL 3.0 14.4 + - - +
621A LEU* 1.3 90.3 - - - +
623A GLY* 1.3 59.9 + - - +
629A ARG* 3.7 2.0 - - - +
1013A MET* 3.9 7.9 - - + -
1017A PHE* 3.9 15.0 - - + -
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Residues in contact with GLY 623 (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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463A ALA* 4.5 11.0 - - - +
464A LYS* 3.4 9.1 - - - -
619A ASN* 3.1 22.2 + - - -
622A MET* 1.3 79.7 - - - +
624A ASP* 1.3 61.4 + - - -
625A LYS 3.4 2.9 - - - -
629A ARG* 2.2 34.3 + - - +
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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