Contacts of the strand formed by residues 514 - 520 (chain B) in PDB entry 3V4R
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 514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447B ARG* 3.5 20.2 - - + +
449B LEU* 3.7 35.9 - - + -
491B LEU* 4.3 0.4 - - + -
511B ILE* 3.2 39.6 + - + +
513B GLU* 1.3 74.5 - - - +
515B SER* 1.4 59.8 + - - +
516B LEU 3.7 24.7 - - - +
517B VAL* 4.4 3.1 - - + -
540B ARG 3.9 17.6 - - - +
541B ALA* 4.3 8.1 - - - +
543B ARG 5.5 0.2 + - - -
544B ASN* 3.2 18.2 + - - +
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Residues in contact with SER 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B ARG* 3.3 20.3 + - - +
446B GLU* 3.2 26.3 - - - +
447B ARG 3.2 4.1 + - - -
513B GLU 3.4 1.8 + - - -
514B VAL* 1.4 71.9 - - - +
516B LEU* 1.4 58.9 + - - +
541B ALA* 4.9 2.2 - - - -
544B ASN* 3.4 29.4 - - - -
546B GLU* 3.5 11.1 - - - +
547B GLY* 4.3 2.0 - - - -
548B ARG* 2.9 29.0 + - - +
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Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B LEU* 5.2 2.2 - - + -
437B GLU* 3.8 20.4 - - + -
438B ILE 4.9 0.4 - - - +
441B ARG* 3.5 42.0 - - + +
447B ARG 3.6 2.0 + - - -
448B VAL* 3.4 34.7 - - + +
449B LEU 3.1 24.1 + - - -
514B VAL* 3.6 5.4 - - - +
515B SER* 1.4 80.0 + - - +
517B VAL* 1.3 74.3 + - - +
518B ALA* 5.2 4.7 - - + -
548B ARG* 3.4 18.8 - - + +
550B ILE* 3.7 27.1 - - + -
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Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LEU* 3.4 13.7 - - + +
451B THR* 4.9 2.2 - - + -
504B LEU* 4.9 4.0 - - + -
514B VAL* 4.4 5.8 - - + -
516B LEU* 1.3 79.1 - - - +
518B ALA* 1.3 62.7 + - - +
519B ILE* 4.1 12.6 - - + -
537B THR* 3.9 38.4 - - + +
540B ARG* 4.1 11.9 - - + +
541B ALA* 3.8 28.5 - - + +
548B ARG 3.2 5.7 + - - -
549B VAL* 3.4 14.9 - - + +
550B ILE 2.9 25.6 + - - +
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Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B LEU* 3.5 33.2 - - + -
448B VAL* 4.9 4.3 - - + -
449B LEU 2.9 12.8 + - - +
450B VAL* 3.4 8.8 - - + +
451B THR* 3.0 27.1 + - - +
516B LEU* 4.2 3.5 - - + -
517B VAL* 1.3 71.5 - - - +
519B ILE* 1.3 63.1 + - - +
520B LEU* 3.5 4.2 + - + +
550B ILE* 3.5 9.4 - - + +
552B TYR* 4.4 10.8 - - + -
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Residues in contact with ILE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B THR* 3.7 17.0 - - + -
517B VAL* 4.1 5.4 - - + -
518B ALA* 1.3 69.3 - - - +
520B LEU* 1.4 59.6 + - - +
522B ALA* 3.7 19.8 - - + +
529B ARG* 3.8 33.4 - - - +
534B LEU* 4.1 14.4 - - + -
537B THR* 3.9 22.9 - - + -
538B ILE* 4.6 4.7 - - + -
549B VAL* 3.9 23.1 - - + -
550B ILE 2.8 13.8 + - - +
551B MET* 4.2 19.3 - - + -
552B TYR* 3.0 27.1 + - - -
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B GLN* 3.9 27.6 - - + +
431B ILE* 5.5 7.4 - - + -
434B LEU* 4.2 20.9 - - + -
450B VAL* 4.4 11.9 - - + -
451B THR 3.0 15.3 + - - +
452B THR* 3.9 28.7 - - + -
457B MET* 5.8 2.7 - - + +
461B LEU* 5.4 8.5 - - + -
518B ALA* 3.5 2.7 + - + +
519B ILE* 1.4 70.0 - - - +
521B ASP* 1.4 71.7 + - + +
529B ARG* 3.2 20.6 + - - -
552B TYR* 3.5 28.5 - - + -
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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