Contacts of the helix formed by residues 584 - 595 (chain X) in PDB entry 6AH0
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 584 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384X GLY 5.0 3.4 + - - -
385X LYS* 4.9 10.8 - - - +
580X ASP 4.4 2.6 + - - -
581X GLU* 3.1 15.5 + - - +
582X ALA 3.5 2.1 - - - +
583X GLU* 1.3 79.4 - - - +
585X PRO* 1.3 52.5 - - - +
586X GLU 3.6 2.6 + - - -
587X LYS 3.9 1.2 + - - -
588X MET* 2.9 31.8 + - - -
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Residues in contact with PRO 585 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385X LYS 5.4 1.8 - - - -
427X GLN* 5.4 6.1 - - - -
583X GLU 3.7 1.6 - - - +
584X ASP* 1.3 64.3 - - - +
586X GLU* 1.3 61.4 + - - +
587X LYS 3.2 2.2 - - - -
589X LEU* 2.7 35.5 + - - +
590X ALA 3.7 0.5 + - - -
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Residues in contact with GLU 586 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584X ASP 3.6 0.8 - - - -
585X PRO* 1.3 76.0 - - - +
587X LYS* 1.3 57.5 - - - +
590X ALA* 4.0 9.9 + - - -
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Residues in contact with LYS 587 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581X GLU 5.6 2.2 + - - -
584X ASP 3.9 2.2 + - - -
586X GLU* 1.3 74.3 - - - +
588X MET* 1.3 62.3 + - - +
589X LEU 3.3 1.3 - - - -
590X ALA* 3.4 2.5 + - - +
591X ASN* 3.0 23.4 + - - -
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Residues in contact with MET 588 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427X GLN 2.9 22.8 - - - +
428X ASN* 4.7 0.9 - - - -
581X GLU 4.9 1.6 + - - -
582X ALA* 4.1 11.5 + - - +
584X ASP 2.9 18.3 + - - -
587X LYS* 1.3 73.8 - - - +
589X LEU* 1.3 60.4 + - - +
591X ASN* 3.2 2.6 + - - +
592X PHE 2.8 23.4 + - - -
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Residues in contact with LEU 589 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426X LEU 4.8 2.9 - - - +
427X GLN* 3.7 15.1 + - - +
585X PRO* 2.7 28.5 + - - +
588X MET* 1.3 69.5 - - - +
590X ALA* 1.3 63.3 + - - +
592X PHE* 3.1 2.3 + - - +
593X GLU* 3.0 20.1 + - - -
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Residues in contact with ALA 590 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585X PRO 3.7 4.6 + - - -
586X GLU 4.0 7.3 + - - -
587X LYS* 3.4 6.9 + - - +
588X MET 3.3 0.4 - - - -
589X LEU* 1.3 75.9 - - - +
591X ASN* 1.3 61.8 + - - +
593X GLU* 3.5 1.9 + - - +
594X SER* 3.4 19.8 + - - -
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Residues in contact with ASN 591 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587X LYS 3.0 14.7 + - - -
588X MET* 3.2 4.5 + - - +
589X LEU 3.1 0.2 - - - -
590X ALA* 1.3 75.8 - - - +
592X PHE* 1.3 65.7 + - - +
593X GLU 3.3 0.2 + - - -
594X SER* 3.4 7.8 + - - -
595X GLY 3.4 13.7 + - - -
598X LYS* 3.8 16.6 - - - +
599X TYR 5.6 2.0 - - - +
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Residues in contact with PHE 592 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426X LEU 5.2 5.6 - - - -
428X ASN* 5.0 13.6 - - - +
588X MET 2.8 18.0 + - - -
589X LEU* 3.1 4.4 + - - +
591X ASN* 1.3 71.1 - - - +
593X GLU* 1.3 63.3 + - - +
595X GLY* 3.0 19.6 + - - -
598X LYS* 5.8 0.4 - - - +
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Residues in contact with GLU 593 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589X LEU 3.0 14.4 + - - -
590X ALA* 3.5 3.1 + - - +
591X ASN 3.2 0.4 - - - -
592X PHE* 1.3 76.6 - - - +
594X SER* 1.3 61.2 + - - +
595X GLY* 3.4 1.7 + - - -
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Residues in contact with SER 594 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590X ALA 3.4 11.5 + - - -
591X ASN* 3.4 10.4 + - - -
592X PHE 3.3 0.6 - - - -
593X GLU* 1.3 76.4 - - - +
595X GLY* 1.3 51.3 + - - +
596X LYS* 2.7 19.3 + - - -
597X HIS* 4.0 6.4 + - - -
598X LYS* 4.9 6.5 - - - -
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Residues in contact with GLY 595 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452X TRP* 6.2 1.6 - - - -
591X ASN 3.4 5.6 + - - -
592X PHE* 3.0 19.1 + - - -
593X GLU 4.1 1.6 - - - -
594X SER* 1.3 72.1 - - - +
596X LYS* 1.3 64.8 + - - +
597X HIS 3.2 1.1 + - - -
598X LYS* 3.4 13.3 + - - +
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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