Contacts of the strand formed by residues 514 - 520 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A ARG* 3.3 25.4 - - + +
449A LEU* 3.7 35.9 - - + -
491A LEU* 4.1 1.1 - - + -
511A ILE* 3.2 38.9 + - + +
513A GLU* 1.4 73.2 - - - +
515A SER* 1.3 59.5 - - - +
516A LEU 3.7 20.4 - - - +
517A VAL* 4.4 3.1 - - + -
540A ARG 3.8 16.5 - - - +
541A ALA* 4.3 8.4 - - - +
544A ASN* 3.2 18.1 + - - +
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Residues in contact with SER 515 (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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441A ARG* 3.3 20.6 + - - +
446A GLU* 3.2 27.8 - - - +
447A ARG 3.1 4.3 + - - -
513A GLU 3.4 1.8 + - - -
514A VAL* 1.3 71.3 - - - +
516A LEU* 1.4 58.9 + - - +
541A ALA* 5.0 2.5 - - - -
544A ASN* 3.4 30.3 - - - -
546A GLU* 3.5 12.1 - - - +
547A GLY* 4.3 1.3 - - - -
548A ARG* 3.0 27.5 + - - +
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Residues in contact with LEU 516 (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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434A LEU* 5.3 2.5 - - + -
437A GLU* 3.8 19.7 - - + -
438A ILE 4.9 0.2 - - - +
441A ARG* 3.5 41.5 - - + +
447A ARG 3.6 2.2 + - - -
448A VAL* 3.4 34.5 - - + +
449A LEU 3.0 24.1 + - - -
514A VAL* 3.6 6.2 - - - +
515A SER* 1.4 81.7 + - - +
517A VAL* 1.3 73.8 + - - +
518A ALA* 4.7 4.7 - - + +
548A ARG* 3.4 19.1 - - + +
550A ILE* 3.7 27.6 - - + -
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Residues in contact with VAL 517 (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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449A LEU* 3.3 14.8 - - + +
504A LEU* 4.2 7.2 - - + -
514A VAL* 4.4 5.2 - - + -
516A LEU* 1.3 79.6 - - - +
518A ALA* 1.3 61.0 + - - +
519A ILE* 4.1 13.0 - - + -
537A THR* 3.9 37.5 - - + +
540A ARG* 4.0 12.1 - - + +
541A ALA* 3.7 29.2 - - + +
548A ARG 3.1 5.9 + - - -
549A VAL* 3.4 14.0 - - + +
550A ILE 2.9 25.8 + - - +
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Residues in contact with ALA 518 (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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434A LEU* 3.5 32.5 - - + -
448A VAL* 4.9 3.4 - - + -
449A LEU 2.9 9.3 + - - -
450A VAL* 3.4 16.8 - - + +
451A THR* 3.0 27.0 + - - -
516A LEU* 4.2 4.4 - - + -
517A VAL* 1.3 71.9 - - - +
519A ILE* 1.3 62.0 + - - +
520A LEU 3.6 1.0 + - - +
550A ILE* 3.5 9.6 - - + +
552A TYR* 4.4 10.5 - - + -
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Residues in contact with ILE 519 (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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451A THR* 4.3 5.4 - - - +
517A VAL* 4.1 7.0 - - + -
518A ALA* 1.3 71.2 - - - +
520A LEU* 1.4 58.4 + - - +
522A ALA* 3.7 18.4 - - + +
529A ARG* 3.5 35.0 - - - +
534A LEU* 4.1 13.7 - - + -
537A THR* 3.9 32.3 - - + -
538A ILE* 4.5 4.5 - - + -
549A VAL* 3.8 24.9 - - + -
550A ILE 2.8 13.4 + - - +
551A MET* 4.2 17.9 - - + -
552A TYR* 3.0 26.9 + - - -
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Residues in contact with LEU 520 (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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430A GLN* 4.6 11.7 - - - +
431A ILE* 5.9 5.4 - - + -
434A LEU* 6.0 2.7 - - + -
450A VAL* 4.8 8.7 - - + -
451A THR 3.2 19.0 + - - +
452A THR* 4.3 16.7 - - + -
518A ALA 3.6 2.4 + - - -
519A ILE* 1.4 69.3 - - - +
521A ASP* 1.4 67.7 + - + +
529A ARG* 3.0 24.1 + - - -
552A TYR* 4.2 14.3 - - + -
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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