Contacts of the helix formed by residues 529 - 537 (chain A) in PDB entry 2YEV
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 529 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A SER* 4.3 5.6 - - - +
273A ARG 4.5 0.2 + - - -
274A LYS* 3.7 1.8 - - - +
275A PRO* 3.6 41.9 - - - +
276A LEU* 5.2 1.3 - - + +
502A TYR* 3.5 61.4 + - + -
503A THR* 5.5 2.2 - - + -
527A SER* 3.1 9.6 + - - +
528A GLU* 1.3 92.3 + - + +
530A PRO* 1.3 66.8 - - - +
531A LEU 3.3 2.7 - - - -
532A TYR* 2.9 41.1 + - + +
533A ASP* 3.2 16.2 + - - +
76B GLN* 2.6 32.7 + - - +
78B HIS* 4.9 5.5 - - - -
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Residues in contact with PRO 530 (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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186A MET* 5.2 3.4 - - + -
190A LYS 5.3 1.8 - - - +
192A PRO* 6.3 1.1 - - + -
502A TYR 3.5 8.3 - - - +
503A THR* 4.6 2.2 - - + -
504A LEU* 3.8 27.1 - - + +
525A PHE* 4.1 14.6 - - + -
526A PRO* 5.9 1.6 - - + -
527A SER 4.2 5.8 - - - +
528A GLU 3.3 10.5 - - - +
529A ARG* 1.3 89.1 - - - +
531A LEU* 1.3 63.1 + - - +
533A ASP* 3.2 7.7 + - + +
534A TRP* 3.0 65.6 + - + +
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Residues in contact with LEU 531 (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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497A ASN* 4.2 5.8 - - - +
501A GLY 3.7 17.0 - - - +
502A TYR* 3.0 23.9 + - + +
503A THR 3.4 22.9 - - - +
504A LEU* 4.3 11.7 - - + +
506A TRP* 4.0 21.8 - - + +
507A LEU* 4.0 31.0 - - + -
530A PRO* 1.3 76.7 - - - +
532A TYR* 1.3 59.6 + - - +
534A TRP* 4.2 12.8 - - + -
535A LYS* 3.4 24.9 + - - +
541A LEU* 6.1 0.2 - - + -
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Residues in contact with TYR 532 (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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502A TYR* 3.8 27.8 + + + +
527A SER* 5.8 0.2 - - - -
529A ARG* 2.9 42.3 + - + +
531A LEU* 1.3 80.5 - - - +
533A ASP* 1.3 78.5 + - - +
535A LYS* 3.9 5.3 - - + +
536A LYS* 3.3 47.5 + - + +
73B GLU* 2.4 43.6 + - + -
76B GLN* 3.6 23.9 - - + +
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Residues in contact with ASP 533 (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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526A PRO* 3.7 31.6 - - + +
527A SER* 2.7 42.8 + - - +
529A ARG 3.2 10.2 + - - +
530A PRO* 3.2 5.7 + - + +
532A TYR* 1.3 91.7 - - - +
534A TRP* 1.3 66.8 + - + +
536A LYS* 3.4 7.9 - - - +
537A LYS* 3.3 26.0 + - + +
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Residues in contact with TRP 534 (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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504A LEU* 3.7 24.2 - - + -
507A LEU* 4.4 6.1 - - + -
521A LEU* 4.2 11.9 - - + -
522A PRO* 3.6 45.6 - - + +
524A GLU* 3.0 25.1 + - + +
525A PHE* 3.7 34.7 - + - +
526A PRO* 4.8 3.1 - - + +
530A PRO* 3.0 34.6 + - + +
531A LEU* 4.3 10.8 - - + +
533A ASP* 1.3 81.5 - - + +
535A LYS* 1.3 63.3 + - - +
536A LYS 3.1 0.2 - - - -
537A LYS* 3.3 7.4 + - + -
539A VAL* 3.1 50.9 + - + +
541A LEU* 4.7 10.3 - - + -
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Residues in contact with LYS 535 (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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531A LEU 3.4 19.1 + - - +
532A TYR* 3.9 6.1 - - + +
533A ASP 3.4 0.4 - - - -
534A TRP* 1.3 78.6 - - - +
536A LYS* 1.3 68.3 + - + +
538A GLY* 3.3 12.2 + - - -
539A VAL 5.7 0.9 - - - -
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Residues in contact with LYS 536 (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 TYR* 3.3 39.7 + - + +
533A ASP* 3.4 13.0 - - - +
534A TRP 3.1 0.4 - - - -
535A LYS* 1.3 87.8 - - + +
537A LYS* 1.3 62.3 + - + +
538A GLY 3.1 1.3 + - - -
73B GLU* 3.2 30.8 + - - -
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Residues in contact with LYS 537 (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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524A GLU* 5.3 15.8 - - + +
526A PRO* 6.0 5.4 - - + -
533A ASP* 3.3 13.2 + - + +
534A TRP* 3.3 4.4 + - + +
536A LYS* 1.3 79.1 - - + +
538A GLY* 1.3 62.6 + - - +
539A VAL* 3.2 29.1 + - + +
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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