Contacts of the helix formed by residues 580 - 588 (chain A) in PDB entry 6C90
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 ASN 580 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A LEU* 3.9 9.9 - - - +
574A LEU* 5.5 2.5 - - + -
579A ILE* 1.3 82.9 - - - +
581A PRO* 1.3 78.2 - - + +
582A GLU* 3.3 18.5 + - - +
583A TYR* 3.0 31.2 + - - +
584A MET 3.9 2.1 + - - -
1103A MG 4.3 0.2 - - - -
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Residues in contact with PRO 581 (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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565A LEU* 5.3 3.4 - - + +
569A MET* 6.2 0.4 - - + -
570A VAL* 3.6 42.0 - - + +
573A LEU* 3.7 18.7 - - + +
574A LEU* 3.7 22.4 - - + +
580A ASN* 1.3 88.6 - - + +
582A GLU* 1.3 66.8 + - - +
584A MET* 3.2 12.8 + - - +
585A LEU* 3.2 15.1 + - - +
851A LEU* 3.7 28.5 - - + -
855A LYS* 5.2 2.5 - - + +
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Residues in contact with GLU 582 (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 ASN* 3.1 30.6 + - - +
581A PRO* 1.3 77.0 - - - +
583A TYR* 1.3 62.1 + - - +
585A LEU* 3.3 6.4 + - - +
586A GLU* 3.1 32.9 + - - +
848A MET* 3.6 28.4 - - + +
851A LEU* 3.4 24.4 - - + +
852A LYS* 4.2 6.6 + - - +
855A LYS* 3.5 20.0 + - - -
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Residues in contact with TYR 583 (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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271A ILE* 4.1 11.8 + - + -
299A LEU* 4.8 11.4 + - - +
579A ILE* 3.9 23.8 - - + -
580A ASN* 3.0 24.6 + - - +
582A GLU* 1.3 78.3 - - - +
584A MET* 1.3 66.5 + - + +
586A GLU* 3.4 4.6 + - - +
587A LYS* 3.1 65.4 + - + +
659B PRO* 3.7 32.3 - - + +
660B ILE* 3.3 29.3 - - + +
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Residues in contact with MET 584 (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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237A TYR* 3.7 17.5 - - - +
268A GLU* 3.6 29.6 - - - +
271A ILE* 3.8 27.6 - - + -
272A LEU* 3.5 35.7 - - + -
563A PHE* 3.9 17.4 - - + -
569A MET* 4.0 14.4 - - - +
573A LEU* 3.7 21.5 - - + -
579A ILE* 5.6 1.1 - - + -
580A ASN 3.9 1.4 + - - -
581A PRO 3.2 4.4 + - - +
583A TYR* 1.3 85.5 - - + +
585A LEU* 1.3 62.5 + - - +
587A LYS 3.7 1.3 - - - +
588A SER* 3.0 23.0 + - - -
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Residues in contact with LEU 585 (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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563A PHE* 3.8 6.0 - - + -
565A LEU* 3.5 28.0 - - + -
581A PRO 3.2 11.9 + - - +
582A GLU* 3.6 8.1 - - - +
583A TYR 3.3 0.2 - - - -
584A MET* 1.3 76.7 - - - +
586A GLU* 1.3 62.2 + - - +
588A SER* 2.9 24.0 + - - -
591A GLN* 3.4 8.8 - - - +
845A VAL* 4.8 6.3 - - + -
846A LEU 4.4 5.6 - - - +
847A GLN* 3.0 60.1 - - + +
848A MET* 4.2 13.2 - - + -
851A LEU* 3.8 31.9 - - + -
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Residues in contact with GLU 586 (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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92A LEU 5.6 0.2 - - - +
93A ALA* 5.0 12.7 - - - +
94A ASP 5.3 2.6 + - - -
95A LEU 5.2 4.7 + - - +
298A HIS* 4.7 6.1 + - - -
582A GLU* 3.1 19.2 + - - +
583A TYR* 3.4 5.8 + - - +
585A LEU* 1.3 75.8 - - - +
587A LYS* 1.3 74.6 + - + +
588A SER 3.5 0.9 - - - +
591A GLN* 3.6 22.5 - - + +
592A PHE* 5.2 1.0 + - - +
595A TYR* 4.4 11.4 - - - +
845A VAL* 3.8 32.9 - - + +
848A MET* 4.3 11.7 - - + +
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Residues in contact with LYS 587 (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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95A LEU* 5.4 8.7 + - - +
271A ILE* 3.6 13.9 - - + +
295A TRP* 2.8 28.9 + - - +
298A HIS* 3.7 35.1 + - + +
299A LEU* 3.7 24.4 - - + +
301A LYS* 5.0 6.9 - - - +
583A TYR* 3.1 55.9 + - + +
584A MET 3.4 3.6 + - - +
585A LEU 3.2 0.8 - - - -
586A GLU* 1.3 89.3 + - - +
588A SER* 1.3 62.4 + - - +
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Residues in contact with SER 588 (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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267A GLU* 3.7 11.2 - - - -
271A ILE* 3.9 5.6 - - - -
295A TRP* 3.5 3.0 + - - -
563A PHE* 3.7 27.2 - - - -
584A MET 3.0 12.9 + - - -
585A LEU 2.9 19.0 + - - -
586A GLU 4.4 0.5 - - - +
587A LYS* 1.3 81.9 - - - +
589A PHE* 1.3 62.1 + - - +
590A TYR* 3.7 6.1 + - - +
591A GLN* 3.1 17.7 + - - +
592A PHE* 3.1 17.5 + - - +
847A GLN* 4.1 2.6 + - - -
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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