Contacts of the helix formed by residues 575 - 586 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556B GLN* 3.7 23.8 + - - +
574B PHE* 1.3 82.4 - - - +
576B LEU* 1.3 70.8 + - - +
577B GLU* 3.9 13.0 + - - +
578B SER* 2.8 31.2 + - - -
579B CYS* 3.0 16.6 - - - +
662B ASP* 4.0 9.1 + - - -
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Residues in contact with LEU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B VAL* 4.9 7.0 - - + -
553B LYS* 4.3 28.0 - - + +
556B GLN* 3.6 30.3 + - + +
575B SER* 1.3 76.3 - - - +
577B GLU* 1.3 61.3 + - - +
578B SER* 1.9 27.0 + - - -
579B CYS* 2.2 26.7 + - + +
580B ARG* 3.7 19.5 - - + +
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Residues in contact with GLU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575B SER* 3.9 17.2 + - - +
576B LEU* 1.3 81.4 + - - +
578B SER* 1.4 66.8 - - - +
580B ARG* 3.5 20.6 - - - +
581B SER* 3.0 18.9 + - - -
666B ARG* 5.8 0.2 - - - -
767B ASP* 3.9 29.8 - - + +
768B THR 5.9 0.2 - - - +
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Residues in contact with SER 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B PHE* 3.6 12.5 - - - +
575B SER* 2.8 33.6 + - - -
576B LEU 1.9 11.6 + - - -
577B GLU* 1.4 78.3 - - - +
579B CYS* 1.3 58.8 + - - -
580B ARG 2.7 0.3 + - - -
581B SER* 2.7 21.8 + - - -
582B MET* 3.0 15.9 + - - -
662B ASP* 4.1 15.9 - - - -
665B VAL* 6.1 2.0 - - - -
666B ARG* 4.2 25.9 - - - +
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Residues in contact with CYS 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B VAL* 5.4 5.4 - - + +
555B LEU* 4.7 9.2 - - + -
556B GLN* 4.4 24.2 - - + +
574B PHE* 5.4 3.4 - - + -
575B SER 3.0 19.1 - - - +
576B LEU* 2.2 22.4 + - + +
578B SER* 1.3 71.1 + - - +
580B ARG* 1.3 53.0 + - - +
582B MET* 2.8 27.0 + - + +
583B VAL* 2.6 33.1 - - + +
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Residues in contact with ARG 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B VAL* 5.6 7.0 - - + -
576B LEU* 3.1 19.8 + - + +
577B GLU* 3.1 28.6 + - - +
578B SER 2.7 1.2 + - - -
579B CYS* 1.3 78.9 - - - +
581B SER* 1.3 51.7 + - - +
583B VAL* 2.6 31.0 - - - +
584B ASN* 3.9 5.5 - - - +
702B LEU* 5.0 22.4 - - - +
840B ARG* 3.0 38.3 + - - +
843B SER 5.3 2.4 - - - +
853B ASN* 4.9 12.5 + - - +
857B CYS* 4.8 5.9 - - - -
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Residues in contact with SER 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B GLU 3.0 8.5 + - - -
578B SER* 2.7 9.7 + - - -
580B ARG* 1.3 74.3 - - - +
582B MET* 1.3 51.8 + - - -
583B VAL 2.5 24.9 + - - +
584B ASN* 4.9 2.7 - - - -
585B LEU* 3.3 16.3 + - - +
666B ARG* 5.8 3.6 - - - -
669B VAL* 4.8 5.8 - - - +
670B ARG* 4.5 19.3 - - - -
673B ILE* 4.3 23.0 - - - +
702B LEU* 5.2 13.5 - - - +
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Residues in contact with MET 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574B PHE* 5.3 8.7 - - + -
578B SER* 3.0 11.6 + - - +
579B CYS* 2.8 32.2 + - + +
581B SER* 1.3 70.1 - - - +
583B VAL* 1.3 58.3 + - + +
585B LEU* 3.9 7.9 - - + -
586B MET* 3.3 29.5 + - - +
594B LEU* 5.5 1.6 - - - +
602B LEU* 3.3 34.4 - - + +
605B ARG* 5.9 0.2 - - + -
606B ILE* 3.1 46.7 - - + -
609B TYR* 4.9 6.7 - - + -
665B VAL* 4.2 21.5 - - + +
666B ARG* 6.3 0.2 - - - -
669B VAL* 4.7 20.8 - - + +
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Residues in contact with VAL 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B SER 5.3 0.2 - - - -
552B VAL* 4.6 25.8 - - + +
579B CYS* 2.6 31.6 - - + +
580B ARG* 2.6 22.7 - - - +
581B SER 2.7 7.6 - - - +
582B MET* 1.3 76.9 - - + +
584B ASN* 1.2 72.2 + - - +
585B LEU 3.0 3.1 - - - +
586B MET* 4.5 5.2 - - - +
587B ASP* 5.2 2.2 - - - +
594B LEU* 3.6 33.4 - - + -
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Residues in contact with ASN 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B ARG 3.9 7.0 - - - +
581B SER* 4.6 2.7 - - - +
583B VAL* 1.2 81.6 - - - +
585B LEU* 1.4 63.1 + - - +
586B MET 4.3 1.5 - - - +
587B ASP* 4.4 13.1 + - - +
673B ILE* 5.3 7.1 - - - +
702B LEU 4.5 16.5 - - - -
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Residues in contact with LEU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B SER 3.3 17.4 + - - +
582B MET* 3.7 7.0 - - + +
583B VAL 3.0 5.3 + - - -
584B ASN* 1.4 79.0 - - - +
586B MET* 1.3 106.4 - - + +
602B LEU* 5.6 2.9 - - + -
605B ARG* 4.4 6.7 - - - -
609B TYR* 5.1 0.9 - - - +
669B VAL* 4.4 18.6 - - + -
672B GLU* 3.3 44.9 - - + +
673B ILE* 3.7 29.7 - - + +
676B LYS* 5.6 4.9 - - + -
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Residues in contact with MET 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582B MET 3.3 19.9 + - - +
583B VAL* 4.5 3.3 - - - +
584B ASN 3.8 0.4 - - - +
585B LEU* 1.3 140.1 - - + +
587B ASP* 1.3 77.6 + - + +
594B LEU* 5.1 11.0 - - + -
598B GLU* 4.9 12.8 - - + +
601B ILE* 4.7 7.9 - - - +
602B LEU* 4.0 37.2 - - + -
605B ARG* 4.0 20.4 - - - +
672B GLU* 4.2 2.9 - - - +
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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