Contacts of the helix formed by residues 582 - 598 (chain A) in PDB entry 6QNW
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 ARG 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ILE* 3.6 14.7 - - + +
460A MET* 4.1 22.4 - - - +
463A VAL* 3.3 38.8 - - - +
464A TYR* 5.6 1.4 - - - -
579A MET 4.4 5.1 + - - -
580A GLU 4.6 0.9 - - - -
581A MET* 1.3 74.2 - - - +
583A ARG* 1.3 58.9 + - - +
584A CYS 3.1 0.4 - - - -
585A LEU* 2.9 44.8 + - + +
586A LEU 3.7 2.1 + - - -
512B PHE* 3.4 39.6 - - + -
550B LEU* 4.0 23.9 + - + +
553B LYS* 3.1 39.1 - - - +
554B ASP* 6.0 4.4 - - - +
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Residues in contact with ARG 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A TRP* 4.3 10.3 - - + -
580A GLU* 3.3 45.6 + - - +
581A MET* 3.0 0.8 - - - -
582A ARG* 1.3 79.2 - - - +
584A CYS* 1.3 61.1 + - - +
586A LEU* 2.9 17.4 + - + +
587A GLN* 2.9 24.8 + - - +
25B THR* 3.6 40.9 - - + +
26B GLY* 5.3 3.1 - - - +
509B LEU* 3.1 28.5 + - + +
510B PRO 3.1 8.0 + - - -
511B SER* 3.3 32.7 + - - +
512B PHE* 3.8 23.9 - - + +
513B GLY 5.4 0.2 - - - +
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Residues in contact with CYS 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ILE* 4.0 1.8 - - + -
577A TRP* 5.4 4.7 - - - -
581A MET* 2.9 23.8 + - - +
583A ARG* 1.3 76.3 - - - +
585A LEU* 1.3 55.1 + - - +
587A GLN* 4.2 1.8 - - - -
588A SER* 2.7 31.7 + - - -
641A LEU* 3.7 4.0 - - - +
644A SER* 3.3 40.4 + - - +
645A VAL* 3.6 27.6 - - + -
648A SER* 3.6 22.7 - - - -
25B THR* 4.8 1.3 + - - -
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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
----------------------------------------------------------
423A ILE* 5.0 15.9 - - + -
425A LEU* 5.4 6.3 - - + -
446A PHE* 4.0 7.3 - - + -
450A VAL* 3.9 20.9 - - + -
456A THR* 4.9 8.5 - - + +
459A ILE* 4.2 13.2 - - + -
582A ARG* 2.9 29.4 + - + +
584A CYS* 1.3 74.2 - - - +
586A LEU* 1.3 66.9 + - - +
588A SER* 2.9 7.3 + - - -
589A LEU* 2.9 20.3 + - - +
641A LEU* 3.6 24.0 - - + -
546B MET* 4.1 19.3 - - + -
550B LEU* 4.8 13.0 - - + -
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Residues in contact with LEU 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ARG 3.7 0.8 + - - +
583A ARG* 2.9 19.4 + - + +
585A LEU* 1.3 73.6 - - - +
587A GLN* 1.3 65.1 + - - +
589A LEU* 2.9 7.5 + - - +
590A GLN* 2.8 23.2 + - - +
509B LEU* 3.8 25.4 - - + -
510B PRO* 5.6 3.1 - - + +
512B PHE* 4.4 14.1 - - + -
543B THR* 3.5 21.3 - - + +
546B MET* 3.6 17.9 - - + -
547B ALA* 3.5 39.3 - - + +
550B LEU* 3.7 25.4 - - + -
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Residues in contact with GLN 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ARG 2.9 18.7 + - - +
586A LEU* 1.3 70.3 - - - +
588A SER* 1.3 65.4 + - - +
590A GLN* 2.9 30.1 - - - +
591A GLN* 2.8 33.3 + - - +
644A SER* 2.6 32.7 + - - +
19B SER 4.4 4.6 + - - +
22B PHE* 2.6 32.3 + - - +
23B PRO 3.5 16.1 + - - +
24B TYR 3.7 10.1 + - - -
25B THR* 3.6 20.2 + - - +
509B LEU* 3.8 7.4 - - + +
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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
----------------------------------------------------------
446A PHE* 3.7 19.1 - - - -
584A CYS 2.7 19.6 + - - -
585A LEU* 2.9 9.0 + - - -
587A GLN* 1.3 75.8 - - - +
589A LEU* 1.3 53.0 + - - +
591A GLN* 3.0 20.6 + - - +
592A ILE* 2.7 39.1 + - - +
640A LEU* 3.5 7.6 + - - -
641A LEU* 3.2 29.4 + - - -
644A SER* 4.1 1.2 - - - -
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Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 4.7 8.3 - - + +
443A ARG* 4.7 4.7 - - + -
446A PHE* 3.6 39.2 - - + -
585A LEU 2.9 11.3 + - - +
586A LEU* 2.9 9.8 + - - +
588A SER* 1.3 76.2 - - - +
590A GLN* 1.3 51.1 + - - +
592A ILE* 2.9 11.9 + - + +
593A GLU* 2.5 39.5 + - + +
542B ALA* 3.4 38.6 - - + +
543B THR* 3.7 13.2 - - + +
546B MET* 3.7 28.3 - - + -
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Residues in contact with GLN 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A LEU 2.8 12.4 + - - +
587A GLN* 2.9 42.4 - - + +
589A LEU* 1.3 72.6 - - - +
591A GLN* 1.3 58.9 + - + +
593A GLU* 3.0 3.1 + - - +
594A SER* 2.7 33.4 + - - -
19B SER* 4.6 13.6 + - - +
504B ASN* 4.9 4.8 + - - -
507B MET* 3.1 46.2 + - + +
509B LEU* 3.2 18.5 - - - +
539B LEU* 6.0 1.1 - - + -
540B GLY 6.0 1.6 - - - +
543B THR* 3.5 22.6 + - + +
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Residues in contact with GLN 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A GLN* 2.8 25.8 + - - +
588A SER* 3.0 37.9 + - - +
590A GLN* 1.3 72.7 - - + +
592A ILE* 1.3 59.6 + - - +
594A SER* 4.4 1.8 - - - -
595A MET* 3.5 26.2 + - - +
640A LEU* 3.4 41.2 + - + +
643A LYS* 5.9 1.6 - - - +
644A SER* 4.7 6.1 - - - +
17B ALA* 4.9 0.9 - - - +
19B SER* 3.3 43.1 + - - +
20B THR* 3.4 26.2 - - + +
22B PHE 5.2 0.2 - - - +
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Residues in contact with ILE 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 4.5 15.3 - - + -
588A SER 2.7 21.2 + - - +
589A LEU* 3.3 17.3 - - + +
591A GLN* 1.3 73.7 - - - +
593A GLU* 1.3 66.1 + - - +
594A SER 3.3 0.2 - - - -
595A MET* 2.9 30.6 + - + +
596A ILE* 3.0 34.9 + - + +
611A PHE* 5.0 5.8 - - + -
612A PHE* 4.9 13.7 - - + -
633A ILE* 6.2 1.1 - - + -
636A VAL* 4.2 12.3 - - + -
637A CYS* 4.3 15.3 - - - -
640A LEU* 3.6 26.2 - - + -
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Residues in contact with GLU 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 3.3 27.0 + - - +
589A LEU* 2.5 21.8 + - + +
590A GLN* 3.0 5.8 + - - +
592A ILE* 1.3 73.3 - - + +
594A SER* 1.3 63.3 + - - +
596A ILE* 2.9 19.8 + - + +
597A GLU* 3.0 22.7 + - - +
540B GLY* 3.2 21.0 + - - -
541B PRO* 3.1 11.8 - - - +
542B ALA* 2.7 35.8 + - + +
543B THR* 2.4 37.5 + - - -
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Residues in contact with SER 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLN 2.7 20.0 + - - -
591A GLN 4.5 2.0 - - - -
593A GLU* 1.3 71.5 - - - +
595A MET* 1.3 55.6 + - - +
597A GLU* 2.9 7.1 + - - +
598A ALA* 2.6 44.0 + - - +
15B GLN 4.9 0.2 + - - -
16B ASN 3.2 16.7 + - - -
17B ALA* 5.1 0.2 - - - -
19B SER* 4.3 14.8 + - - -
502B VAL* 4.4 17.1 - - - +
504B ASN* 5.3 0.8 + - - -
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Residues in contact with MET 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A GLN 3.5 20.6 - - - +
592A ILE* 2.9 32.9 + - + +
594A SER* 1.3 77.1 - - - +
596A ILE* 1.3 61.9 + - - +
599A GLU* 3.2 30.4 - - + +
600A SER* 4.2 0.7 + - - -
611A PHE* 3.8 26.8 - - + -
619A TRP* 5.7 2.5 - - + +
636A VAL* 4.8 5.6 - - + -
640A LEU* 4.3 9.2 - - + -
8B LEU* 3.9 22.0 - - + -
12B VAL* 4.5 11.9 - - + -
16B ASN 3.5 19.3 - - - +
17B ALA* 3.6 22.2 - - + -
20B THR* 5.7 0.9 - - - -
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Residues in contact with ILE 596 (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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442A ARG* 3.4 51.4 - - + +
592A ILE* 3.2 31.9 - - + +
593A GLU* 2.9 11.1 + - - +
595A MET* 1.3 78.7 - - - +
597A GLU* 1.3 58.9 + - - +
600A SER* 3.1 24.5 - - - -
606A ASP* 3.8 5.7 - - - +
607A MET 3.9 14.8 - - - +
608A THR* 4.3 8.3 - - + +
611A PHE* 3.6 30.5 - - + -
612A PHE* 5.1 9.9 - - + -
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Residues in contact with GLU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 3.4 29.3 + - - +
593A GLU* 3.0 20.7 + - - +
594A SER* 2.9 7.2 + - - +
596A ILE* 1.3 78.1 - - - +
598A ALA* 1.3 57.0 + - - +
599A GLU 3.3 0.9 - - - -
600A SER 3.0 0.7 + - - -
601A SER* 2.5 39.7 + - - -
606A ASP* 4.6 7.4 - - - +
540B GLY* 4.2 6.7 - - - -
541B PRO* 3.6 20.8 - - - +
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Residues in contact with ALA 598 (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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594A SER* 2.6 29.7 + - - +
597A GLU* 1.3 74.1 - - - +
599A GLU* 1.3 60.3 + - - +
600A SER 3.3 0.5 + - - -
601A SER* 3.4 19.1 + - - +
602A VAL* 5.1 1.9 + - - +
15B GLN 4.9 2.5 - - - +
16B ASN* 3.4 30.0 + - - +
501B PHE 5.1 11.4 - - - +
502B VAL* 5.7 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
------------------------------------------------------------
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