Contacts of the helix formed by residues 632 - 650 (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 SER 632 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LYS* 4.2 27.5 + - - -
617A GLU 4.8 5.2 - - - -
618A THR* 5.1 2.9 - - - +
619A TRP* 4.5 2.7 - - - -
631A GLY* 1.3 75.5 - - - +
633A ILE* 1.3 68.1 + - - +
634A GLY* 3.5 7.0 + - - -
635A LYS* 3.4 33.7 + - - +
636A VAL* 3.5 21.0 + - - +
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Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU* 6.5 0.7 - - + -
592A ILE* 6.2 1.3 - - + -
611A PHE* 3.7 19.7 - - + +
612A PHE* 3.4 48.2 - - + -
613A GLU 4.4 1.1 - - - +
614A ASN 3.8 21.3 - - - +
615A LYS* 4.0 26.2 - - + +
617A GLU 4.4 1.3 - - - +
619A TRP* 3.3 32.8 - - + -
632A SER* 1.3 75.7 - - - +
634A GLY* 1.3 62.2 + - - +
636A VAL* 3.0 8.4 + - + +
637A CYS* 2.9 30.0 + - - -
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Residues in contact with GLY 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A GLU* 3.4 30.7 - - - +
615A LYS* 4.7 5.2 - - - +
632A SER* 3.5 4.7 + - - -
633A ILE* 1.3 77.5 - - - +
635A LYS* 1.3 57.4 + - - +
637A CYS* 3.3 7.9 + - - +
638A ARG* 2.9 45.0 + - - +
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Residues in contact with LYS 635 (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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415A CYS* 5.5 2.1 - - + +
621A ILE* 3.6 28.3 - - + -
631A GLY* 5.2 1.3 - - - -
632A SER* 3.4 29.4 + - - +
633A ILE 3.2 0.2 - - - -
634A GLY* 1.3 76.6 - - - +
636A VAL* 1.3 53.0 + - - +
638A ARG* 3.5 24.5 + - - +
639A THR* 2.5 40.3 + - - +
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Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A ILE* 4.2 11.0 - - + -
595A MET* 4.8 3.8 - - + -
619A TRP* 3.6 36.8 - - + +
621A ILE* 4.0 11.9 - - + -
632A SER 3.5 14.8 + - - +
633A ILE* 3.0 13.0 + - + +
635A LYS* 1.3 75.3 - - - +
637A CYS* 1.3 66.4 + - - +
639A THR* 3.3 6.1 + - - -
640A LEU* 2.9 39.0 + - + +
8B LEU* 3.7 25.8 - - + -
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Residues in contact with CYS 637 (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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446A PHE* 4.2 22.3 - - + -
449A GLU* 4.7 10.8 - - + -
450A VAL* 4.1 21.1 - - + +
592A ILE* 4.3 18.6 - - - -
612A PHE* 4.3 22.9 - - - -
633A ILE* 2.9 21.8 + - - -
634A GLY* 3.3 10.3 + - - +
636A VAL* 1.3 78.1 - - - +
638A ARG* 1.3 56.6 + - + +
640A LEU* 3.8 3.1 - - - +
641A LEU* 2.9 28.8 + - - +
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Residues in contact with ARG 638 (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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415A CYS* 3.4 31.4 + - + +
417A LEU* 3.7 31.2 - - - +
449A GLU* 3.1 49.5 + - - +
450A VAL* 4.7 2.9 - - - -
453A CYS* 3.7 26.6 - - + +
634A GLY* 2.9 30.7 + - - +
635A LYS* 3.6 31.0 - - - +
637A CYS* 1.3 74.9 - - - +
639A THR* 1.3 57.4 + - - +
641A LEU* 3.7 6.8 - - - +
642A ALA* 2.9 32.4 + - - +
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Residues in contact with THR 639 (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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411A PHE* 3.8 7.0 - - + -
415A CYS* 4.0 12.5 - - - +
621A ILE* 4.5 11.1 - - + +
635A LYS* 2.5 30.2 + - - +
636A VAL* 3.3 7.2 + - - -
638A ARG* 1.3 77.2 - - - +
640A LEU* 1.3 59.5 + - + +
643A LYS* 2.9 30.3 + - - +
3B VAL* 3.7 32.5 - - + +
5B PRO* 3.8 29.4 - - + -
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER* 3.5 10.0 + - - +
591A GLN* 3.4 27.4 + - + +
592A ILE* 3.6 34.1 - - + -
595A MET* 4.3 9.9 - - + -
636A VAL* 2.9 26.5 + - + +
637A CYS* 3.9 3.4 - - - +
639A THR* 1.3 78.2 - - + +
641A LEU* 1.3 63.6 + - - +
643A LYS* 3.3 13.8 + - + +
644A SER* 3.0 21.3 + - - -
5B PRO* 5.0 9.9 - - + +
8B LEU* 5.3 8.3 - - + -
20B THR* 4.0 26.0 - - + -
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Residues in contact with LEU 641 (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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446A PHE* 5.4 0.2 - - + -
450A VAL* 3.5 29.4 - - + -
453A CYS* 4.3 9.9 - - + -
455A ALA* 3.6 23.6 - - + -
456A THR* 3.7 14.1 - - - +
459A ILE* 4.0 13.2 - - + -
584A CYS 3.7 16.8 - - - +
585A LEU* 3.6 26.0 - - + -
588A SER* 3.2 12.9 + - - +
637A CYS 2.9 18.0 + - - +
638A ARG* 3.7 4.7 - - - +
640A LEU* 1.3 77.0 - - - +
642A ALA* 1.3 56.1 - - - +
644A SER* 3.2 3.6 + - - -
645A VAL* 2.9 31.4 + - - +
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Residues in contact with ALA 642 (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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411A PHE* 3.5 21.3 - - + -
414A ALA* 3.9 31.0 - - + +
415A CYS* 4.3 1.3 - - - -
455A ALA* 3.8 13.7 - - + -
638A ARG 2.9 18.3 + - - +
641A LEU* 1.3 76.2 - - - +
643A LYS* 1.3 56.9 + - - +
645A VAL* 3.7 2.0 - - - +
646A PHE* 2.9 34.7 + - + +
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Residues in contact with LYS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A PHE* 3.8 11.8 - - + -
591A GLN* 5.9 1.6 - - - +
639A THR 2.9 19.2 + - - +
640A LEU* 3.6 15.3 - - + +
641A LEU 3.2 0.2 - - - -
642A ALA* 1.3 77.0 - - - +
644A SER* 1.3 58.8 + - - +
646A PHE 3.8 0.3 - - - -
647A ASN* 2.9 52.2 + - - +
699A TRP* 3.8 14.7 - - + -
703A ASN* 4.2 14.8 + - - -
5B PRO* 3.8 31.4 - - + -
6B THR* 5.2 7.6 - - - -
20B THR* 2.9 31.9 + - - +
21B THR* 4.8 5.0 + - - +
23B PRO* 5.3 1.4 - - - +
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Residues in contact with SER 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A CYS* 3.3 35.4 + - - +
587A GLN* 2.6 30.9 + - - -
588A SER* 4.1 2.7 - - - -
591A GLN* 4.7 4.5 - - - +
640A LEU 3.0 16.9 + - - -
641A LEU 3.6 3.8 - - - -
643A LYS* 1.3 75.4 - - - +
645A VAL* 1.3 57.4 + - - +
647A ASN* 3.3 12.7 + - - +
648A SER* 2.9 22.7 + - - -
23B PRO 4.7 1.4 - - - +
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Residues in contact with VAL 645 (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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455A ALA* 4.0 10.1 - - + +
458A TYR* 4.1 25.1 - - + -
459A ILE* 3.5 37.2 - - + +
581A MET* 5.3 5.2 - - - -
584A CYS* 3.6 13.0 - - + -
641A LEU* 2.9 24.8 + - + +
642A ALA* 3.7 6.7 - - - +
644A SER* 1.3 77.0 - - - +
646A PHE* 1.3 60.7 + - + +
648A SER* 2.8 19.2 + - - -
649A LEU* 2.9 33.2 + - + +
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Residues in contact with PHE 646 (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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284A LEU* 3.8 20.0 - - + -
407A ILE* 4.8 3.1 - - + -
410A GLU* 3.9 24.5 - - + -
411A PHE* 3.7 33.0 - + + -
414A ALA* 3.9 16.8 - - + -
458A TYR* 4.1 19.1 - + - -
642A ALA* 2.9 17.4 + - - +
645A VAL* 1.3 78.5 - - + +
647A ASN* 1.3 57.2 + - - +
649A LEU* 3.8 13.2 - - + -
650A TYR* 2.7 48.5 + + + +
699A TRP* 3.4 45.1 - + + -
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Residues in contact with ASN 647 (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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643A LYS* 2.9 53.1 + - - +
644A SER* 3.4 10.9 - - - +
645A VAL 3.2 0.2 - - - -
646A PHE* 1.3 76.2 - - - +
648A SER* 1.3 62.0 + - - +
651A ALA* 3.2 24.8 - - - +
655A LEU* 3.4 11.3 - - + +
699A TRP* 2.5 36.4 + - - +
703A ASN* 4.8 0.5 + - - +
23B PRO* 3.7 41.8 + - + +
24B TYR* 3.5 7.7 - - - -
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Residues in contact with SER 648 (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 TRP* 3.2 55.3 + - - +
578A GLY 5.1 0.2 + - - -
581A MET* 3.6 26.8 - - - +
584A CYS* 3.6 17.8 - - - -
644A SER 2.9 11.5 + - - -
645A VAL 2.8 10.5 + - - -
647A ASN* 1.3 77.1 - - - +
649A LEU* 1.3 60.2 + - - +
651A ALA* 3.4 7.8 - - - +
23B PRO 5.3 0.4 + - - -
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Residues in contact with LEU 649 (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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279A ARG* 5.8 2.3 + - - -
280A SER* 4.2 19.7 - - - -
281A LYS* 5.5 10.1 + - + +
282A PHE* 4.8 13.7 - - + -
284A LEU* 3.5 39.9 - - + -
458A TYR* 5.3 4.7 - - + -
581A MET* 3.9 22.2 - - + -
645A VAL* 2.9 50.1 + - + +
646A PHE* 3.8 11.7 - - + -
648A SER* 1.3 75.5 - - - +
650A TYR* 1.3 67.0 + - + +
651A ALA* 3.1 8.8 + - - +
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Residues in contact with TYR 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLN* 3.1 35.9 + - + +
279A ARG* 4.9 18.3 + - + +
280A SER* 4.0 24.9 - - - -
284A LEU* 3.7 22.3 - - + +
406A TRP* 3.7 12.7 - + - -
407A ILE* 4.1 19.5 - - + +
410A GLU* 4.7 0.3 - - - +
646A PHE* 2.7 45.1 + + + +
647A ASN 4.0 0.4 - - - -
649A LEU* 1.3 77.4 - - + +
651A ALA* 1.3 64.0 + - - +
652A SER* 3.2 11.6 + - - -
655A LEU* 4.4 1.4 - - - +
697A ASP* 3.8 16.3 - - - +
698A PRO* 5.4 4.5 - - + -
699A TRP* 3.9 30.8 - - + -
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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
------------------------------------------------------------
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