Contacts of the strand formed by residues 505 - 512 (chain Y) in PDB entry 5VEB
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 LEU 505 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503Y ASP 4.1 2.0 + - - -
504Y GLN* 1.3 75.0 + - - +
506Y ILE* 1.3 62.6 + - - +
507Y GLN* 3.5 25.6 - - - +
508Y THR* 3.9 15.0 - - - +
548Y GLY* 3.6 20.9 - - - -
549Y ILE 3.6 6.7 - - - +
550Y LEU* 3.8 14.3 - - + +
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Residues in contact with ILE 506 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494Y THR* 3.8 20.4 + - + -
495Y PHE 3.8 17.1 - - - +
496Y VAL* 4.1 12.6 - - + -
497Y CYS 5.7 0.2 - - - +
504Y GLN* 3.9 16.6 - - + +
505Y LEU* 1.3 78.7 - - - +
507Y GLN* 1.3 64.4 + - - +
537Y PHE* 4.2 8.7 - - + -
549Y ILE* 2.8 40.3 + - + +
550Y LEU* 4.8 0.4 - - - +
551Y THR* 3.9 18.4 - - + -
586Y VAL* 3.7 30.1 - - + -
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Residues in contact with GLN 507 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493Y GLU 4.4 5.3 + - - -
494Y THR* 3.1 43.2 + - + +
505Y LEU* 3.5 9.6 - - - +
506Y ILE* 1.3 82.6 + - + +
508Y THR* 1.3 88.7 + - - +
509Y LEU* 4.5 3.1 - - + -
549Y ILE* 2.8 39.4 + - + +
608Y PRO* 3.9 19.7 - - - +
609Y LEU* 3.9 23.7 - - + +
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Residues in contact with THR 508 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505Y LEU* 3.9 20.8 - - - +
507Y GLN* 1.3 83.9 + - - +
509Y LEU* 1.3 73.6 + - - +
510Y HIS* 6.1 0.2 - - + -
542Y ASN* 4.7 3.9 + - - +
546Y THR* 3.9 20.0 - - + +
547Y ALA 3.4 9.4 + - - +
548Y GLY* 4.6 0.7 - - - -
608Y PRO* 3.7 20.2 - - + -
609Y LEU* 3.3 24.4 + - - +
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Residues in contact with LEU 509 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507Y GLN* 4.5 0.7 - - + -
508Y THR* 1.3 76.2 - - - +
510Y HIS* 1.3 60.4 + - - +
511Y ALA 4.3 0.4 - - - -
525Y PHE* 4.0 16.6 - - + -
539Y ILE* 4.4 5.4 - - + -
546Y THR* 3.0 30.4 - - - -
547Y ALA* 2.8 18.5 + - + +
549Y ILE* 3.9 30.5 - - + -
568Y VAL* 4.0 35.4 - - + -
584Y VAL* 3.8 20.6 - - + -
609Y LEU* 3.3 30.1 - - + +
611Y VAL* 4.3 10.3 - - + -
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Residues in contact with HIS 510 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508Y THR* 6.1 0.2 - - + -
509Y LEU* 1.3 75.5 - - - +
511Y ALA* 1.4 70.0 + - - +
512Y VAL* 3.5 25.3 - - + +
525Y PHE* 4.4 1.3 - - - -
544Y ASP 5.0 1.3 - - - -
545Y ASN* 3.2 23.1 + - + -
546Y THR* 3.8 15.4 - - + +
608Y PRO 4.9 10.8 - - - -
609Y LEU 2.8 13.9 + - - +
610Y GLU* 3.4 16.0 - - + -
611Y VAL* 2.8 33.0 + - - +
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Residues in contact with ALA 511 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510Y HIS* 1.4 83.3 + - - +
512Y VAL* 1.4 59.6 + - - +
523Y PHE* 3.8 26.1 - - + -
525Y PHE* 3.5 23.5 - - + -
545Y ASN* 2.8 25.9 + - + +
570Y ILE* 3.7 19.7 - - + -
611Y VAL* 3.4 8.1 - - - -
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Residues in contact with VAL 512 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510Y HIS* 3.5 31.9 - - + +
511Y ALA* 1.4 73.5 - - - +
513Y ASP* 1.3 65.7 + - - +
514Y LYS* 4.1 6.5 - - + +
523Y PHE* 4.7 1.3 - - - -
570Y ILE* 4.5 0.4 - - - +
610Y GLU* 3.4 38.1 - - + +
611Y VAL 2.9 6.3 + - - +
612Y LEU* 3.4 22.7 - - + +
613Y PHE* 2.8 33.6 + - - +
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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