Contacts of the helix formed by residues 586 - 594 (chain C) in PDB entry 5ZR1
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 GLN 586 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274B PHE* 4.6 4.9 - - + -
278B SER* 4.0 16.2 - - - +
281B PHE* 5.4 0.6 - - - +
282B ASN* 3.6 34.3 + - - -
485B PRO* 5.5 5.2 - - - +
495B VAL* 4.1 13.7 - - + -
520C VAL* 5.6 4.2 - - + +
582C ILE* 3.6 12.8 + - - +
583C LEU* 3.8 31.5 + - - +
585C MET* 1.3 78.0 - - - +
587C ALA* 1.3 63.3 + - + +
588C ILE 3.5 0.2 - - - -
589C PHE* 3.8 11.2 - - + +
590C ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C VAL* 3.7 30.3 - - + +
521C LEU* 3.8 21.5 - - + -
524C LEU* 3.8 15.9 - - + -
583C LEU 4.1 0.2 - - - +
584C PHE* 2.9 8.8 + - - +
586C GLN* 1.3 81.4 - - + +
588C ILE* 1.3 59.8 + - - +
589C PHE 3.1 1.6 - - - -
590C ALA 3.8 0.4 - - - +
591C PHE* 3.0 34.7 + - - -
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Residues in contact with ILE 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B MET* 3.8 37.7 - - + +
524C LEU* 3.9 6.2 - - + +
537C ILE* 4.1 20.6 - - + -
540C PHE* 3.6 36.8 - - + -
584C PHE* 2.9 22.7 + - + +
585C MET* 3.7 19.1 - - - -
587C ALA* 1.3 75.7 - - - +
589C PHE* 1.3 62.1 + - - +
591C PHE* 4.0 3.1 + - - +
592C GLU* 3.8 14.4 + - - +
597C ILE* 3.7 25.3 - - + +
599C PHE* 4.9 7.8 - - + -
608C VAL* 5.6 0.4 - - + -
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Residues in contact with PHE 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B GLU 5.0 1.1 - - - -
490B SER* 3.2 33.4 - - - -
493B GLN* 3.4 59.7 - - + -
494B ASP 4.0 8.3 - - - -
495B VAL* 4.0 15.9 - - + -
498B MET 4.0 8.7 - - - +
499B GLY* 3.5 25.6 - - - -
585C MET 3.5 17.6 + - - +
586C GLN* 3.8 8.1 - - + +
587C ALA 3.1 0.2 - - - -
588C ILE* 1.3 80.8 - - - +
590C ALA* 1.3 65.4 + - + +
591C PHE 3.2 0.2 - - - -
592C GLU* 3.2 11.7 + - + +
593C ASN* 3.6 23.6 + - - +
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Residues in contact with ALA 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B PRO 5.9 1.8 - - - +
486B SER* 5.4 7.2 - - - +
521C LEU* 3.7 29.8 - - + -
586C GLN 3.1 19.2 + - - +
587C ALA 3.3 0.6 + - - +
589C PHE* 1.3 81.9 - - + +
591C PHE* 1.3 60.3 + - - +
593C ASN* 3.0 19.4 - - - +
594C MET* 3.3 22.8 - - + +
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Residues in contact with PHE 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C LEU* 3.8 17.0 - - + -
521C LEU* 3.3 44.2 - - + -
524C LEU* 3.7 42.6 - - + -
525C PHE* 4.0 15.0 - + + -
528C TYR* 4.6 10.1 - + + -
540C PHE* 5.8 0.2 - + - -
587C ALA 3.0 12.7 + - - +
588C ILE 4.0 2.0 + - - +
589C PHE 3.2 0.4 - - - -
590C ALA* 1.3 80.1 - - - +
592C GLU* 1.3 58.4 + - - +
594C MET* 4.1 8.7 - - - -
595C GLY 3.5 0.7 + - - -
596C LEU* 2.9 52.2 + - + +
597C ILE* 3.4 29.6 + - + -
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Residues in contact with GLU 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B HIS* 5.0 1.0 - - - -
493B GLN* 5.3 4.9 - - - +
498B MET 3.6 0.2 - - - +
499B GLY* 2.9 36.8 - - - +
500B LYS* 5.1 0.7 - - - -
503B THR* 5.0 2.8 + - - -
588C ILE 3.8 10.3 + - - +
589C PHE* 3.2 11.7 + - + +
591C PHE* 1.3 76.6 - - - +
593C ASN* 1.3 62.8 + - + +
594C MET 3.2 1.6 - - - -
595C GLY* 2.8 21.5 + - - -
597C ILE* 3.8 21.7 - - + +
599C PHE* 3.1 33.7 + - + +
446E PRO* 5.7 7.1 - - + +
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Residues in contact with ASN 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ARG* 5.3 5.6 + - - +
457B ASP* 4.5 12.6 + - - +
458B HIS* 3.8 21.0 + - - +
486B SER* 5.8 1.8 + - - -
489B GLU* 5.5 10.9 + - - +
493B GLN* 4.2 26.7 + - - +
503B THR* 5.9 2.9 - - + -
589C PHE* 3.6 22.2 + - - +
590C ALA* 3.0 22.1 - - - +
592C GLU* 1.3 78.6 - - - +
594C MET* 1.3 60.1 + - - +
595C GLY 3.3 0.2 - - - -
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Residues in contact with MET 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B GLY 5.4 1.1 - - - +
319B VAL* 3.7 33.9 - - + -
320B GLY* 4.2 9.6 - - - +
457B ASP* 3.9 27.4 - - + +
458B HIS* 3.4 3.5 - - - -
459B ILE* 2.8 35.3 + - + +
487C ILE* 5.3 8.1 - - + -
491C LEU* 4.8 5.6 - - - -
521C LEU* 4.1 15.5 - - + -
590C ALA* 3.3 23.2 + - + +
591C PHE* 4.2 22.0 - - + +
592C GLU 3.2 0.4 - - - -
593C ASN* 1.3 81.9 + - - +
595C GLY* 1.3 57.5 + - - +
596C LEU* 4.3 13.9 - - + -
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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