Contacts of the helix formed by residues 575 - 587 (chain A) in PDB entry 1QXP
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 SER 575 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A GLN* 4.0 15.0 - - - +
574A PHE* 1.3 82.1 - - - +
576A LEU* 1.3 51.5 + - - +
577A GLU* 2.6 16.3 + - - -
578A SER* 2.4 32.4 + - - -
579A CYS* 2.8 14.0 + - - -
662A ASP* 4.2 15.5 + - - -
767A ASP* 5.4 2.7 - - - -
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Residues in contact with LEU 576 (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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553A LYS* 5.8 4.3 - - + -
554A GLU* 5.6 7.0 - - - +
556A GLN* 4.2 18.7 - - - +
575A SER* 1.3 70.3 - - - +
577A GLU* 1.4 63.6 + - + +
579A CYS* 3.4 12.6 - - - -
580A ARG* 2.4 43.3 + - - +
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Residues in contact with GLU 577 (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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575A SER* 2.6 11.5 + - - -
576A LEU* 1.4 100.7 + - + +
578A SER* 1.4 51.6 + - - +
580A ARG* 3.7 3.5 - - - +
581A SER* 2.8 32.9 + - - -
666A ARG* 3.8 29.4 + - - +
702A LEU* 5.8 0.9 - - - +
767A ASP* 3.0 38.0 - - + +
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Residues in contact with SER 578 (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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574A PHE* 4.9 4.0 - - - -
575A SER* 2.4 27.4 + - - -
577A GLU* 1.4 66.3 - - - +
579A CYS* 1.3 51.2 - - - -
581A SER* 2.6 12.3 + - - -
582A MET* 2.5 50.6 + - - +
662A ASP* 2.6 29.4 + - - -
665A VAL* 4.7 10.8 - - - -
666A ARG* 3.8 30.0 + - - +
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Residues in contact with CYS 579 (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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553A LYS* 5.0 9.6 - - + -
554A GLU 5.4 0.4 - - - +
555A LEU* 4.2 9.8 - - + +
556A GLN* 3.6 32.1 - - + +
559A LEU* 5.3 0.2 - - - -
574A PHE* 3.7 18.6 - - - -
575A SER 2.8 18.4 + - - +
576A LEU* 3.4 14.1 - - - -
578A SER* 1.3 74.0 - - - +
580A ARG* 1.3 62.6 + - - +
582A MET* 3.0 24.7 + - - +
583A VAL* 2.5 36.9 + - - +
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Residues in contact with ARG 580 (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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553A LYS* 5.0 6.9 - - + +
576A LEU 2.4 23.1 + - - +
577A GLU* 3.7 5.4 - - - +
578A SER 3.3 0.2 - - - -
579A CYS* 1.3 76.1 - - - +
581A SER* 1.3 66.2 + - - +
583A VAL* 3.1 10.1 + - - +
584A ASN* 2.9 31.2 + - - +
702A LEU* 5.7 0.7 - - + -
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Residues in contact with SER 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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577A GLU 2.8 13.9 + - - -
578A SER* 2.6 15.6 + - - -
580A ARG* 1.3 74.1 - - - +
582A MET* 1.4 62.1 + - - -
584A ASN* 3.1 9.2 + - - +
585A LEU* 3.0 20.3 + - - +
666A ARG* 4.8 8.7 - - - -
669A VAL* 3.1 26.4 + - - +
670A ARG* 4.2 13.0 + - - +
673A ILE* 5.1 6.2 - - - +
702A LEU* 4.7 18.2 - - - +
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Residues in contact with MET 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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555A LEU* 3.4 28.5 - - + -
559A LEU* 3.8 9.4 - - + -
574A PHE* 4.8 4.9 - - + -
578A SER* 2.5 32.3 + - - +
579A CYS* 3.3 37.5 - - - +
581A SER* 1.4 73.9 - - - +
583A VAL* 1.4 59.1 + - - +
584A ASN 3.0 4.6 + - - -
585A LEU* 3.6 2.2 + - - +
586A MET* 3.3 17.7 + - - +
602A LEU* 3.3 35.1 - - + +
606A ILE* 3.9 25.8 - - - -
665A VAL* 5.7 5.8 - - - -
669A VAL* 3.8 24.9 - - + -
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Residues in contact with VAL 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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552A VAL 5.6 1.3 - - - +
553A LYS* 4.6 17.7 - - + -
555A LEU* 5.5 6.3 - - + +
579A CYS 2.5 24.6 + - - +
580A ARG* 3.4 12.1 - - - +
582A MET* 1.4 79.6 - - - +
584A ASN* 1.3 56.8 + - - +
586A MET* 3.1 20.7 - - - +
587A ASP 4.5 3.3 + - - +
592A GLY* 5.3 15.4 - - - +
593A LYS 5.6 1.4 + - - -
594A LEU* 6.0 5.6 - - + -
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Residues in contact with ASN 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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580A ARG* 2.9 26.2 + - - +
581A SER* 3.2 11.1 - - - +
583A VAL* 1.3 78.2 - - - +
585A LEU* 1.4 67.2 + - - +
586A MET 3.0 1.9 + - - -
587A ASP* 3.2 20.1 + - - -
588A ARG* 3.9 16.7 + - - +
673A ILE* 5.6 6.1 - - + -
702A LEU* 4.3 36.4 + - + +
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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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581A SER 3.0 7.4 + - - +
582A MET* 3.7 9.2 - - - +
584A ASN* 1.4 76.0 - - - +
586A MET* 1.3 68.2 + - - +
587A ASP* 4.3 2.6 - - - +
588A ARG* 4.8 13.8 + - - +
602A LEU* 5.4 0.9 - - + -
605A ARG* 3.0 58.8 - - - +
669A VAL* 4.4 14.4 - - + +
672A GLU* 4.1 21.1 - - + +
673A ILE* 5.1 16.5 - - + +
676A LYS* 5.9 5.6 - - + -
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Residues in contact with MET 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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582A MET 3.3 7.7 + - - +
583A VAL* 3.1 29.4 - - - +
585A LEU* 1.3 79.4 - - - +
587A ASP* 1.4 76.6 + - - +
593A LYS 5.9 1.6 - - - +
594A LEU* 5.1 17.5 - - + -
598A GLU* 5.9 8.7 - - + -
602A LEU* 5.4 2.8 - - + +
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Residues in contact with ASP 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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583A VAL 5.0 2.8 - - - +
584A ASN* 3.2 12.3 + - - +
585A LEU 4.3 2.2 - - - +
586A MET* 1.4 86.9 - - - +
588A ARG* 1.4 74.6 + - - +
591A ASN* 5.2 6.9 + - - +
592A GLY 6.0 0.3 + - - -
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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