Contacts of the helix formed by residues 597 - 614 (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 VAL 597 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595B GLY 3.3 0.4 - - - -
596B LEU* 1.4 76.9 - - + +
598B GLU* 1.4 90.1 + - - +
599B PHE 3.1 0.7 - - - -
600B ASN* 2.8 32.1 - - - +
601B ILE* 2.9 8.0 + - - +
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Residues in contact with GLU 598 (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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586B MET* 4.9 13.5 - - + +
587B ASP* 3.9 39.5 - - + +
594B LEU* 4.3 11.2 - - + +
595B GLY* 2.9 28.2 - - - -
596B LEU 3.7 0.7 + - - -
597B VAL* 1.4 90.6 + - - +
599B PHE* 1.4 49.3 + - - +
601B ILE* 2.9 9.4 + - - +
602B LEU* 2.6 34.5 + - - +
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Residues in contact with PHE 599 (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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550B ILE 5.2 11.7 - - - +
555B LEU* 5.0 16.6 - - + -
558B ILE* 5.3 12.8 - - + -
559B LEU* 5.7 7.0 - - + -
594B LEU* 4.2 20.1 - - + +
595B GLY* 2.6 28.1 + - - +
596B LEU* 4.7 3.1 - - - -
597B VAL 3.1 0.8 - - - -
598B GLU* 1.4 77.8 - - - +
600B ASN* 1.4 56.0 + - - +
602B LEU* 2.6 46.6 + - + +
603B TRP* 3.1 29.9 + + + -
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Residues in contact with ASN 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B LEU 4.8 4.8 + - - +
597B VAL* 2.8 31.4 + - - +
599B PHE* 1.4 77.8 - - - +
601B ILE* 1.4 60.2 + - - +
602B LEU 3.0 2.5 + - - -
603B TRP* 3.5 4.7 + - - +
604B ASN* 2.6 38.3 + - - +
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Residues in contact with ILE 601 (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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523B ASP 5.1 0.9 - - - +
524B GLU* 3.4 44.9 - - + +
526B VAL* 4.1 21.8 - - - +
586B MET* 4.9 7.0 - - - -
597B VAL 2.9 14.7 + - - +
598B GLU* 2.9 6.5 + - - +
600B ASN* 1.4 74.9 - - - +
602B LEU* 1.3 65.1 + - - +
604B ASN* 2.9 42.7 - - + +
605B ARG* 3.7 22.1 + - + +
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Residues in contact with LEU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B LEU* 5.8 6.5 - - + -
582B MET* 3.3 56.8 - - + +
585B LEU* 5.6 2.7 - - + -
586B MET* 4.0 27.1 - - + -
594B LEU* 5.6 6.1 - - + -
598B GLU 2.6 11.4 + - - +
599B PHE* 2.6 45.6 + - + +
601B ILE 1.3 71.8 - - - +
603B TRP* 1.4 56.1 - - - +
604B ASN 3.1 1.1 - - - -
605B ARG* 3.6 7.8 - - + +
606B ILE* 3.3 29.4 + - + +
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Residues in contact with TRP 603 (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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537B LYS* 6.6 0.4 - - + -
559B LEU* 3.9 35.2 - - + -
574B PHE* 4.5 7.4 - + - -
599B PHE* 3.1 27.5 + + + +
600B ASN* 3.5 5.5 + - - +
602B LEU* 1.4 79.2 - - - +
604B ASN* 1.4 56.8 + - - +
606B ILE* 4.0 24.5 - - + -
607B ARG* 3.1 43.5 + - + +
610B LEU* 4.0 21.1 - - + -
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Residues in contact with ASN 604 (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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600B ASN* 2.6 35.1 + - - +
601B ILE* 2.9 46.2 - - + +
602B LEU 3.1 1.0 - - - -
603B TRP* 1.4 74.3 - - - +
605B ARG* 1.3 56.6 + - - +
607B ARG* 3.4 11.0 + - - +
608B ASN* 3.0 33.4 + - - +
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Residues in contact with ARG 605 (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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521B LEU* 4.5 12.5 - - - +
522B PRO* 4.0 29.0 + - + +
582B MET* 5.9 0.2 - - + -
585B LEU* 4.4 4.0 - - - -
586B MET* 4.0 29.3 - - - +
601B ILE* 3.7 15.0 + - + +
602B LEU* 3.6 14.8 - - + +
604B ASN* 1.3 71.3 - - - +
606B ILE* 1.3 58.3 + - + +
607B ARG 2.8 1.9 + - - -
608B ASN* 3.1 9.1 + - - +
609B TYR* 2.7 69.2 + - + +
672B GLU* 2.3 48.6 + - - -
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Residues in contact with ILE 606 (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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559B LEU* 5.4 2.2 - - + -
574B PHE* 3.5 39.7 - - + -
582B MET* 3.1 49.1 - - + -
602B LEU* 3.3 23.6 + - + +
603B TRP* 4.0 26.7 - - + +
605B ARG* 1.3 78.2 - - - +
607B ARG* 1.3 68.7 + - - +
609B TYR* 3.1 12.7 + - + +
610B LEU* 2.9 34.0 + - + +
661B PHE* 4.0 4.3 - - + -
665B VAL* 5.1 0.9 - - + -
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Residues in contact with ARG 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B TRP* 3.1 41.4 + - + +
604B ASN* 3.7 12.0 + - - +
605B ARG 2.8 3.0 - - - -
606B ILE* 1.3 75.3 - - - +
608B ASN* 1.3 93.8 + - - +
610B LEU* 2.6 57.0 + - + +
611B THR* 3.0 18.6 + - - +
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Residues in contact with ASN 608 (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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522B PRO* 5.6 4.3 - - - +
604B ASN 3.0 13.2 + - - +
605B ARG* 3.2 13.2 - - - +
607B ARG* 1.3 86.7 - - - +
609B TYR* 1.4 68.7 + - + -
610B LEU 3.2 0.7 + - - -
611B THR* 3.2 22.7 + - - -
612B ILE* 3.4 9.7 + - - +
636B ALA* 6.0 1.7 - - - -
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Residues in contact with TYR 609 (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* 4.9 8.1 - - + -
585B LEU* 5.1 1.0 - - - +
605B ARG* 2.7 69.5 + - + +
606B ILE* 3.9 10.8 - - + +
608B ASN* 1.4 76.7 - - - +
610B LEU* 1.4 57.0 + - - +
612B ILE* 3.4 4.8 + - - +
613B PHE* 3.2 23.6 + - - +
636B ALA* 4.9 7.9 - - + -
638B PHE* 5.9 3.2 - + - -
661B PHE* 3.9 0.9 - - - -
664B PHE* 3.2 16.4 - - + -
665B VAL* 3.4 45.5 - - + -
668B LEU* 3.2 37.2 - - + -
669B VAL* 3.8 20.7 + - + +
672B GLU* 3.3 8.1 + - - +
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Residues in contact with LEU 610 (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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603B TRP* 4.0 18.2 - - + -
606B ILE* 2.9 27.0 + - + +
607B ARG* 2.6 47.2 + - + +
609B TYR* 1.4 69.6 - - - +
611B THR* 1.3 63.4 + - - +
612B ILE 3.4 1.0 + - - -
613B PHE* 3.7 2.1 + - - +
614B ARG* 3.2 32.8 + - + +
661B PHE* 3.2 28.0 - - + -
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Residues in contact with THR 611 (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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607B ARG* 3.0 27.9 + - - +
608B ASN* 3.2 19.3 + - - -
610B LEU* 1.3 80.8 - - - +
612B ILE* 1.3 56.8 + - - -
614B ARG* 4.1 7.0 - - - +
615B LYS* 3.2 28.5 + - + +
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Residues in contact with ILE 612 (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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608B ASN 3.4 7.4 + - - +
609B TYR* 3.4 11.9 + - - +
611B THR* 1.3 75.0 - - - +
613B PHE* 1.4 66.0 + - - +
614B ARG 3.2 0.2 - - - -
615B LYS* 3.2 15.9 + - - +
616B PHE* 3.6 12.3 - - - +
632B ALA* 4.7 6.3 - - + +
635B ALA* 4.6 22.2 - - + -
636B ALA* 5.7 2.7 - - + +
664B PHE* 4.4 14.1 - - + -
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Residues in contact with PHE 613 (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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609B TYR 3.2 13.0 + - - +
610B LEU 3.8 8.1 - - - +
612B ILE* 1.4 75.6 - - - +
614B ARG* 1.3 91.5 + - - +
616B PHE* 2.9 30.7 + - - +
617B ASP* 3.2 15.4 + - + -
622B GLY 3.6 4.7 - - - -
623B SER* 3.2 34.5 - - - -
624B MET* 3.3 26.7 - - + -
660B ASP 4.1 0.9 - - - -
661B PHE* 3.5 47.1 - + + -
664B PHE* 4.0 18.8 - + + -
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Residues in contact with ARG 614 (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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610B LEU* 3.2 23.9 + - + +
611B THR* 4.2 7.0 - - - +
612B ILE 3.2 0.2 - - - -
613B PHE* 1.3 105.9 - - - +
615B LYS* 1.3 59.5 + - + +
616B PHE 2.9 7.7 + - - -
617B ASP* 3.8 19.9 + - - +
618B LEU* 3.3 23.0 + - - +
620B LYS* 5.1 12.5 - - - +
622B GLY* 4.7 10.1 - - - +
661B PHE* 5.8 2.4 - - - +
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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
------------------------------------------------------------
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