Contacts of the helix formed by residues 565 - 575 (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 PRO 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU* 6.2 1.3 - - + -
209A VAL* 3.7 30.3 - - + -
212A VAL* 3.9 34.1 - - + -
215A TYR* 4.7 1.3 - - + -
563A SER 4.6 1.8 - - - +
564A GLU* 1.3 99.8 - - + +
566A TRP* 1.3 59.9 + - - +
567A THR* 3.9 12.3 - - - +
568A LEU* 3.1 15.7 + - + +
569A ALA* 2.9 24.9 + - - +
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Residues in contact with TRP 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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206A ASP 5.0 1.6 - - - -
207A TYR* 2.8 40.7 + + - +
208A GLU 5.2 0.4 - - - -
209A VAL* 3.8 16.2 - - + +
217A TYR* 3.7 28.9 - + - -
222A LEU* 6.5 0.2 - - + -
396A ALA* 3.7 38.6 + - + +
397A ASN* 3.6 19.5 - - + +
400A PHE* 3.9 5.2 - + + -
521A TYR* 3.2 35.7 - + - -
564A GLU 3.6 1.4 + - - -
565A PRO* 1.3 73.8 - - - +
567A THR* 1.3 81.5 + - + +
569A ALA* 3.7 0.7 - - - +
570A LEU* 2.9 45.6 + - + +
577A LYS 4.4 2.2 - - - -
578A ASN* 4.0 20.4 - - - -
579A MET* 4.8 2.2 - - + -
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Residues in contact with THR 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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209A VAL* 5.0 0.4 - - + -
215A TYR* 3.1 46.5 + - - +
216A ASP 5.0 0.9 - - - +
217A TYR* 4.5 9.6 - - + -
565A PRO* 3.9 4.2 - - - +
566A TRP* 1.3 111.7 - - + +
568A LEU* 1.3 62.3 + - - +
570A LEU* 3.3 3.2 + - - +
571A GLU* 2.9 29.3 + - - +
576A ALA 4.0 3.1 - - - +
577A LYS* 3.3 28.4 - - + +
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Residues in contact with LEU 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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212A VAL* 5.5 3.6 - - + -
215A TYR* 4.0 44.0 - - + +
560A LEU* 5.2 0.2 - - + -
564A GLU* 3.7 38.6 - - + +
565A PRO* 3.1 19.6 + - + +
567A THR* 1.3 80.8 + - - +
569A ALA* 1.3 57.3 + - - +
571A GLU* 3.2 3.5 + - - +
572A ASN* 2.9 57.7 + - - +
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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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396A ALA* 4.1 20.0 - - + -
400A PHE* 4.3 1.6 - - + -
557A MET* 3.5 32.3 - - + +
560A LEU* 4.2 22.2 - - + -
561A GLY 5.6 0.7 - - - +
564A GLU* 5.1 3.6 - - + +
565A PRO 2.9 15.8 + - - +
566A TRP 3.7 4.3 - - - +
568A LEU* 1.3 78.0 - - - +
570A LEU* 1.3 62.1 + - - +
572A ASN* 3.4 11.4 + - - +
573A VAL* 3.5 5.4 - - - +
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Residues in contact with LEU 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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400A PHE* 4.3 9.8 - - + -
521A TYR* 4.1 24.7 - - + -
524A GLN* 4.0 11.2 - - + +
525A PHE* 3.6 27.8 - - + -
566A TRP* 2.9 24.8 + - + +
567A THR 3.7 3.1 - - - +
569A ALA* 1.3 73.4 - - - +
571A GLU* 1.3 60.9 + - - +
573A VAL* 3.2 6.0 - - - +
574A VAL* 2.9 47.9 + - + +
576A ALA 3.6 9.4 - - - +
577A LYS 4.5 0.2 - - - -
578A ASN 3.5 36.6 - - - +
579A MET 4.1 1.6 - - - +
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Residues in contact with GLU 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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215A TYR* 2.7 27.2 + - - -
567A THR 2.9 18.1 + - - +
568A LEU* 3.2 6.5 + - - +
570A LEU* 1.3 74.4 - - - +
572A ASN* 1.3 71.0 + - - +
573A VAL 3.9 0.2 - - - -
575A GLY* 2.9 36.1 + - - +
576A ALA 3.3 17.2 + - - +
577A LYS* 3.3 32.3 + - - +
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Residues in contact with ASN 572 (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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553A LYS* 4.7 10.5 - - - +
556A ASN* 4.6 12.0 + - + +
557A MET* 5.1 6.3 - - + +
560A LEU* 3.8 26.6 - - + +
568A LEU* 2.9 39.6 + - - +
569A ALA* 3.5 9.9 - - - +
570A LEU 3.3 0.4 - - - -
571A GLU* 1.3 81.2 - - - +
573A VAL* 1.3 59.0 + - + +
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Residues in contact with VAL 573 (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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525A PHE* 3.4 39.3 - - + -
528A ALA* 3.3 15.6 - - + +
529A LEU* 4.2 20.0 - - + -
553A LYS* 3.1 44.0 + - + +
554A LEU* 5.1 5.2 - - + -
557A MET* 4.5 11.9 - - + -
569A ALA 3.5 11.4 - - - +
570A LEU 3.2 16.8 - - - +
572A ASN* 1.3 79.5 - - - +
574A VAL* 1.3 61.0 + - + +
575A GLY 3.7 0.7 - - - -
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A GLN* 3.7 34.8 - - + +
525A PHE* 3.6 30.1 - - + -
528A ALA* 4.0 7.2 - - + -
553A LYS* 6.0 0.2 - - - -
570A LEU* 2.9 37.3 + - + +
573A VAL* 1.3 83.6 - - + +
575A GLY* 1.3 60.9 + - - +
576A ALA* 3.5 21.1 - - + +
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Residues in contact with GLY 575 (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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571A GLU* 2.9 28.3 + - - +
573A VAL 3.7 0.4 - - - -
574A VAL* 1.3 77.9 - - - +
576A ALA* 1.3 59.0 + - - +
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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