Contacts of the helix formed by residues 552 - 571 (chain A) in PDB entry 2VWJ
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 ASP 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A ASN* 3.6 8.7 - - - +
551A ALA* 1.3 76.0 - - - +
553A ALA* 1.3 66.9 + - - +
554A GLU* 3.6 18.0 + - - +
555A THR* 2.5 29.0 + - - -
556A VAL* 3.0 21.7 + - - +
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Residues in contact with ALA 553 (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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399A ASN* 3.4 30.2 - - - +
552A ASP* 1.3 74.9 - - - +
554A GLU* 1.3 66.0 + - + +
556A VAL* 3.4 1.2 + - - +
557A LYS* 3.1 36.3 + - - +
582A PHE* 3.7 16.4 - - + -
599A GLU* 4.8 4.7 - - - +
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Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ASP* 3.4 10.1 + - - +
553A ALA* 1.3 77.5 - - + +
555A THR* 1.3 64.1 + - - +
557A LYS* 3.4 7.7 + - - +
558A LYS* 3.0 24.8 + - - +
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Residues in contact with THR 555 (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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548A ILE* 5.8 1.8 - - + -
551A ALA* 4.2 12.1 - - + -
552A ASP* 2.5 39.7 + - - -
554A GLU* 1.3 75.0 - - - +
556A VAL* 1.3 66.6 + - - +
558A LYS* 3.1 8.9 + - - +
559A LYS* 2.8 37.7 + - + +
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Residues in contact with VAL 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASN* 3.5 33.4 - - + +
401A VAL* 3.8 23.1 - - + +
534A PHE* 3.7 11.4 - - + -
547A THR* 3.9 3.4 - - - +
548A ILE* 3.8 32.3 - - + +
551A ALA* 3.9 10.5 - - + -
552A ASP 3.0 17.7 + - - +
553A ALA 3.9 2.9 - - - +
555A THR* 1.3 75.7 - - - +
557A LYS* 1.3 53.9 + - - +
559A LYS* 3.3 6.4 + - - +
560A ALA* 2.7 33.4 + - - +
582A PHE* 4.4 4.7 - - + -
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Residues in contact with LYS 557 (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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401A VAL* 4.9 1.3 - - - -
553A ALA* 3.1 23.8 + - - +
554A GLU* 3.7 5.8 - - - +
556A VAL* 1.3 73.7 - - - +
558A LYS* 1.3 65.1 + - - +
560A ALA* 3.1 6.7 + - - +
561A LYS* 3.0 35.2 + - + +
579A TYR* 4.1 13.2 - - + +
582A PHE* 3.6 45.5 - - + +
599A GLU* 3.2 28.4 + - - -
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Residues in contact with LYS 558 (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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554A GLU 3.0 13.7 + - - +
555A THR* 3.4 9.9 - - - +
557A LYS* 1.3 75.9 - - - +
559A LYS* 1.3 65.3 + - + +
561A LYS* 3.3 7.2 + - - +
562A GLU* 3.1 39.1 + - - +
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Residues in contact with LYS 559 (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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532A PHE* 4.1 19.5 - - + +
534A PHE* 4.0 20.6 - - + -
548A ILE* 4.5 12.1 - - + -
555A THR* 2.8 30.3 + - + +
556A VAL* 3.6 5.2 - - - +
558A LYS* 1.3 75.5 - - + +
560A ALA* 1.3 62.0 + - - +
562A GLU* 3.3 29.5 + - - +
563A PHE* 3.1 21.8 + - - +
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Residues in contact with ALA 560 (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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401A VAL* 3.9 28.5 - - + -
403A LEU* 5.3 5.1 - - + +
528A ILE* 5.9 1.6 - - + -
534A PHE* 3.8 13.2 - - + -
556A VAL 2.7 21.4 + - - +
557A LYS 3.1 5.3 + - - +
559A LYS* 1.3 71.8 - - - +
561A LYS* 1.3 64.2 + - - +
563A PHE* 3.1 9.6 + - - +
564A LEU* 3.0 23.7 + - - +
579A TYR* 4.2 13.7 - - + -
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Residues in contact with LYS 561 (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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557A LYS* 3.0 20.6 + - - +
558A LYS* 3.7 7.4 - - - +
560A ALA* 1.3 74.8 - - + +
562A GLU* 1.3 65.0 + - - +
564A LEU* 3.0 25.8 + - + +
565A ASP* 3.2 17.6 + - - +
579A TYR* 4.4 33.9 - - + -
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Residues in contact with GLU 562 (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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532A PHE* 4.1 14.2 - - + -
558A LYS* 3.1 33.3 + - - +
559A LYS* 3.3 39.1 + - - +
561A LYS* 1.3 76.4 - - - +
563A PHE* 1.3 63.3 + - - +
565A ASP* 3.4 7.5 + - - +
566A TYR* 3.1 21.0 + - - +
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Residues in contact with PHE 563 (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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403A LEU* 4.2 17.7 - - + -
524A THR* 3.6 24.5 - - + -
527A GLU* 3.9 9.9 - - + -
528A ILE* 3.4 56.8 - - + -
532A PHE* 3.6 37.2 - + + -
534A PHE* 5.1 0.7 - - + -
559A LYS 3.1 13.8 + - - +
560A ALA* 3.1 10.7 + - - +
562A GLU* 1.3 73.8 - - - +
564A LEU* 1.3 63.1 + - - +
566A TYR* 4.2 3.6 - + - -
567A ILE* 2.8 60.6 + - + +
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Residues in contact with LEU 564 (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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403A LEU* 4.9 14.1 - - + -
560A ALA 3.0 12.1 + - - +
561A LYS* 3.0 20.1 + - + +
563A PHE* 1.3 77.8 - - - +
565A ASP* 1.3 60.3 + - - +
567A ILE* 3.9 2.6 - - + +
568A ASN* 2.9 57.7 + - - +
577A LEU* 3.9 32.3 - - + +
578A GLU* 4.2 6.1 - - - +
579A TYR* 3.7 30.7 - - + +
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Residues in contact with ASP 565 (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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561A LYS* 3.2 12.4 + - - +
562A GLU* 3.8 9.0 - - - +
563A PHE 3.3 0.2 - - - -
564A LEU* 1.3 77.0 - - - +
566A TYR* 1.3 67.4 + - - +
568A ASN* 4.0 3.5 - - - +
569A ALA* 2.9 28.0 + - - +
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Residues in contact with TYR 566 (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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527A GLU* 2.8 49.2 + - + -
531A LYS* 3.7 13.8 + - + +
532A PHE* 3.8 31.4 - + + -
562A GLU 3.1 14.1 + - - +
563A PHE* 3.3 7.6 + + - +
565A ASP* 1.3 81.0 - - - +
567A ILE* 1.3 65.5 + - + +
569A ALA* 3.7 4.0 - - - +
570A LYS* 2.9 56.3 + - + +
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Residues in contact with ILE 567 (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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523A THR* 4.8 2.0 - - + -
524A THR* 4.1 18.6 - - + +
527A GLU* 3.7 36.1 - - + -
563A PHE* 2.8 48.6 + - + +
564A LEU* 3.9 6.3 - - - +
566A TYR* 1.3 80.0 - - + +
568A ASN* 1.3 66.5 + - - +
570A LYS* 4.4 6.5 - - + +
571A LEU* 2.9 52.8 + - + +
577A LEU* 4.1 17.3 - - + -
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Residues in contact with ASN 568 (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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564A LEU* 2.9 39.0 + - - +
565A ASP* 4.0 3.1 - - - +
567A ILE* 1.3 79.9 - - - +
569A ALA* 1.3 56.1 + - - +
571A LEU* 4.0 0.7 - - - +
575A LEU 3.9 4.7 - - - +
576A GLU* 3.1 31.5 + - + +
577A LEU* 2.8 42.8 + - - +
1758A K 2.7 28.4 - - - -
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Residues in contact with ALA 569 (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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565A ASP 2.9 18.4 + - - +
566A TYR* 3.7 3.8 - - - +
568A ASN* 1.3 78.6 - - - +
570A LYS* 1.3 61.1 + - - +
571A LEU 3.9 4.0 - - - +
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Residues in contact with LYS 570 (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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523A THR* 6.1 3.3 - - + +
527A GLU* 3.0 24.1 + - + +
531A LYS* 4.5 6.7 - - - +
566A TYR* 2.9 48.5 + - + +
567A ILE* 4.0 9.4 - - + +
569A ALA* 1.3 76.4 - - - +
571A LEU* 1.3 68.5 + - + +
572A PRO* 3.5 4.2 - - - +
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Residues in contact with LEU 571 (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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408A LEU* 4.3 14.4 - - + -
520A TYR* 4.1 25.8 - - + +
523A THR* 4.3 22.4 - - + -
524A THR* 4.2 10.3 - - - +
567A ILE* 2.9 40.7 + - + +
569A ALA 3.9 4.0 - - - +
570A LYS* 1.3 75.9 - - + +
572A PRO* 1.4 74.4 - - + +
573A GLY 3.5 0.9 + - - -
575A LEU* 3.9 24.2 - - + +
576A GLU* 5.1 0.9 - - - -
577A LEU* 4.2 16.2 - - + +
1758A K 2.8 22.5 - - - -
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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