Contacts of the helix formed by residues 581 - 599 (chain A) in PDB entry 6VW1
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 581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A THR* 3.6 36.6 - - + +
232A GLU* 4.5 17.5 - - + +
233A ILE* 3.5 34.8 - - + +
520A LEU* 3.6 20.0 - - + -
580A ASN* 1.3 75.6 + - - +
582A ARG* 1.3 66.3 + - - +
583A PRO* 3.3 3.6 - - - -
584A LEU* 3.1 14.0 + - + +
585A LEU* 3.0 34.2 + - + +
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Residues in contact with ARG 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 5.2 0.2 - - - -
580A ASN* 3.5 13.2 + - - +
581A VAL* 1.3 78.8 - - - +
583A PRO* 1.3 63.2 - - + +
585A LEU* 4.3 11.2 - - + +
586A ASN* 2.8 60.8 + - - +
536B GLU* 2.6 40.7 + - - -
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Residues in contact with PRO 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A PHE* 3.4 31.1 - - + +
524A GLN* 3.7 24.9 - - + +
527A GLU* 4.0 29.8 - - + +
539A LEU* 4.4 5.7 - - + +
580A ASN* 3.7 22.2 - - + +
581A VAL 3.5 3.8 - - - -
582A ARG* 1.3 92.4 - - + +
584A LEU* 1.3 57.8 + - - +
586A ASN* 3.4 2.9 + - + +
587A TYR* 2.9 28.8 + - - +
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Residues in contact with LEU 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ILE* 4.5 6.7 - - + -
236A LEU* 5.5 2.7 - - + -
446A ILE* 4.4 5.2 - - + -
447A VAL* 5.2 3.6 - - + -
450A LEU* 3.7 28.5 - - + -
519A THR* 4.6 5.2 - - + +
520A LEU* 4.5 12.6 - - + -
523A PHE* 3.4 42.4 - - + +
580A ASN 5.2 0.8 + - - +
581A VAL* 3.1 27.6 + - + +
583A PRO* 1.3 77.5 - - - +
585A LEU* 1.3 69.1 + - + +
587A TYR* 3.1 5.6 + - - +
588A PHE* 3.0 55.7 + - + -
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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
----------------------------------------------------------
232A GLU* 4.0 38.1 - - + +
233A ILE* 4.8 11.4 - - + -
236A LEU* 4.0 29.6 - - + +
581A VAL* 3.0 28.0 + - + +
582A ARG* 3.9 9.9 - - + +
584A LEU* 1.3 81.4 - - + +
586A ASN* 1.3 61.7 + - - +
588A PHE* 3.3 3.4 + - - +
589A GLU* 2.8 36.6 + - - +
592A PHE* 5.7 0.3 - - - +
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Residues in contact with ASN 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU* 4.5 11.7 + - - +
539A LEU* 5.4 7.9 + - + +
582A ARG* 2.8 50.6 + - - +
583A PRO* 3.8 4.5 - - + +
585A LEU* 1.3 76.2 - - - +
587A TYR* 1.3 66.5 + - - +
588A PHE 3.4 0.3 + - - -
589A GLU* 3.5 24.0 + - - +
590A PRO* 4.2 4.0 - - - +
536B GLU* 5.9 0.4 + - - -
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Residues in contact with TYR 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 4.6 17.0 - - + +
438A PHE* 4.2 6.1 - - - -
439A LEU* 3.8 25.2 - - + +
442A GLN* 4.0 25.0 + - + +
446A ILE* 5.4 0.7 - - + -
523A PHE* 3.4 32.8 - + + -
526A GLN* 5.2 6.1 - - + -
539A LEU* 4.3 22.4 - - + +
540A HIS* 3.5 44.5 + - + +
583A PRO 2.9 14.5 + - - +
584A LEU 3.3 8.5 - - - +
586A ASN* 1.3 78.6 - - - +
588A PHE* 1.3 91.4 + + - +
590A PRO* 4.0 5.9 - - - +
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Residues in contact with PHE 588 (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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236A LEU* 3.9 20.6 - - + +
439A LEU* 3.5 29.8 - - + -
442A GLN* 4.0 8.7 - - + -
443A ALA* 3.5 32.1 - - + -
446A ILE* 4.3 7.4 - - + -
447A VAL* 3.7 15.3 - - + -
523A PHE* 4.3 4.9 - + - -
584A LEU* 3.0 47.8 + - + +
585A LEU 3.5 2.7 - - - +
587A TYR* 1.3 103.5 - + - +
589A GLU* 1.3 59.4 + - - +
590A PRO* 3.4 4.0 - - - -
591A LEU* 3.2 15.2 + - + +
592A PHE* 2.9 27.0 + - - +
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Residues in contact with GLU 589 (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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585A LEU* 2.8 23.7 + - - +
586A ASN* 3.7 18.3 - - - +
588A PHE* 1.3 76.3 - - - +
590A PRO* 1.3 69.7 - - + +
592A PHE* 3.0 28.5 + - - +
593A THR* 3.0 34.8 + - + +
596A LYS* 5.2 1.6 + - - -
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Residues in contact with PRO 590 (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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436A ILE* 4.6 12.0 - - + +
439A LEU* 4.0 16.8 - - + -
538A PRO* 5.5 6.3 - - + -
540A HIS* 4.7 11.2 - - + +
586A ASN 4.2 3.4 - - - +
587A TYR 4.0 10.3 - - - +
588A PHE 3.5 4.3 - - - -
589A GLU* 1.3 94.9 - - + +
591A LEU* 1.3 61.3 + - - +
593A THR* 2.8 23.8 + - + +
594A TRP* 3.0 11.9 + - - +
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Residues in contact with LEU 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 5.3 3.8 - - + -
240A LEU* 4.9 0.9 - - + -
436A ILE* 4.0 13.0 - - + +
439A LEU* 3.7 24.8 - - + +
440A LEU* 3.8 31.9 - - + +
443A ALA* 3.5 32.1 - - + -
588A PHE* 3.2 16.0 + - + +
590A PRO* 1.3 80.2 - - - +
592A PHE* 1.3 57.6 + - - +
594A TRP* 3.7 13.2 - - + +
595A LEU* 2.9 67.3 + - + +
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Residues in contact with PHE 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PRO* 4.3 14.8 - - + -
236A LEU* 3.5 48.9 - - + +
239A HIS* 3.8 23.1 - + + -
585A LEU 5.7 0.2 - - - +
588A PHE 2.9 14.7 + - - +
589A GLU* 3.0 32.3 + - - +
591A LEU* 1.3 76.8 - - - +
593A THR* 1.3 57.3 + - - +
595A LEU* 3.3 3.6 + - - +
596A LYS* 2.9 65.3 + - + +
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Residues in contact with THR 593 (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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589A GLU* 3.0 27.8 + - + +
590A PRO* 2.8 22.7 + - + +
592A PHE* 1.3 74.7 - - + +
594A TRP* 1.3 62.2 + - - +
596A LYS* 3.3 20.5 + - - +
597A ASP* 3.0 23.7 + - - +
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Residues in contact with TRP 594 (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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243A TYR* 3.8 27.6 - + - -
284A PRO* 3.4 36.8 - - + -
285A PHE* 3.8 24.1 - + - -
436A ILE* 3.8 32.1 - - + -
440A LEU* 5.5 0.2 - - + -
590A PRO 3.0 17.2 + - - +
591A LEU* 3.7 6.5 - - + +
592A PHE 3.3 0.2 - - - -
593A THR* 1.3 78.6 + - - +
595A LEU* 1.3 84.1 + - + +
597A ASP* 3.3 7.9 + - + +
598A GLN* 2.9 65.9 + - + +
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Residues in contact with LEU 595 (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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236A LEU* 4.2 16.4 - - + -
239A HIS* 4.0 16.2 - - + +
240A LEU* 4.0 30.1 - - + +
243A TYR* 4.8 10.8 - - + -
440A LEU* 5.0 5.2 - - + -
591A LEU* 2.9 56.8 + - + +
592A PHE* 3.7 3.8 - - - +
594A TRP* 1.3 98.7 - - + +
596A LYS* 1.3 65.5 + - - +
598A GLN* 3.1 4.9 + - - -
599A ASN* 2.9 34.8 + - - +
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Residues in contact with LYS 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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239A HIS* 3.5 37.0 + - + +
589A GLU* 5.2 1.2 + - - -
592A PHE* 2.9 55.2 + - + +
593A THR* 3.3 19.5 + - - +
595A LEU* 1.3 77.1 - - - +
597A ASP* 1.3 62.9 + - - +
599A ASN* 3.7 6.4 + - - +
600A LYS* 3.7 11.1 + - - +
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Residues in contact with ASP 597 (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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593A THR 3.0 13.7 + - - +
594A TRP* 3.7 10.8 - - + +
596A LYS* 1.3 77.1 - - - +
598A GLN* 1.3 65.3 + - + +
599A ASN 3.2 0.7 + - - -
600A LYS* 3.3 39.8 + - - +
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Residues in contact with GLN 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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243A TYR* 4.3 17.2 - - + -
285A PHE* 6.0 0.4 - - - -
594A TRP* 2.9 63.4 + - + +
595A LEU* 3.1 8.2 + - - +
597A ASP* 1.3 79.7 + - - +
599A ASN* 1.3 64.6 + - - +
600A LYS* 3.4 7.2 + - - +
601A ASN 5.0 1.0 + - - -
602A SER* 4.3 5.5 + - - -
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Residues in contact with ASN 599 (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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239A HIS* 2.9 50.1 + - + +
242A ALA* 3.6 14.6 - - - +
243A TYR* 3.8 22.7 + - - +
595A LEU 2.9 19.9 + - - +
596A LYS 4.0 4.0 - - - +
597A ASP 3.2 0.2 - - - -
598A GLN* 1.3 82.6 - - - +
600A LYS* 1.3 63.7 + - - +
601A ASN 3.2 3.1 - - - -
602A SER* 3.1 30.3 + - - +
604A VAL* 4.2 11.4 - - + +
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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
------------------------------------------------------------
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