Contacts of the strand formed by residues 453 - 459 (chain A) in PDB entry 2VL7
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 PHE 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A LYS* 4.1 9.2 + - - +
386A SER* 3.3 24.7 - - - +
387A VAL 4.6 0.4 - - - +
388A LEU* 3.7 35.2 - - + +
425A MET* 4.7 9.2 - - + -
432A VAL* 6.4 0.2 - - + -
452A LEU* 1.3 111.1 - - + +
454A GLU* 1.3 62.9 + - - +
455A SER 3.6 23.3 - - - +
456A LEU* 4.6 1.6 - - + -
504A ARG 5.7 0.7 - - - -
505A ALA* 3.8 39.7 - - + -
513A VAL* 4.4 20.2 - - + +
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Residues in contact with GLU 454 (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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382A ASN 4.6 1.2 - - - +
383A SER* 3.4 31.2 + - - +
384A SER* 3.3 28.6 + - - -
385A LYS* 3.6 16.8 + - + +
386A SER 3.1 6.0 + - - +
453A PHE* 1.3 75.9 - - - +
455A SER* 1.3 61.2 + - - +
512A TYR 4.6 2.7 - - - +
513A VAL* 4.0 8.8 - - - +
514A LYS* 3.1 58.0 + - + +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 4.2 2.3 - - - +
383A SER* 4.4 2.8 + - - -
386A SER 4.0 1.2 + - - -
387A VAL* 3.3 28.2 - - - +
388A LEU 3.1 23.7 + - - +
453A PHE* 3.5 10.7 - - - -
454A GLU* 1.3 82.1 + - - +
456A LEU* 1.3 60.1 + - - +
457A VAL 4.3 0.2 - - - -
513A VAL* 4.8 0.4 - - - -
514A LYS* 3.2 28.3 - - - -
516A TYR* 3.7 20.6 - - - -
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Residues in contact with LEU 456 (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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388A LEU* 3.4 10.1 - - + -
390A PHE* 3.9 20.9 - - + -
453A PHE* 4.6 4.0 - - + -
455A SER* 1.3 74.1 - - - +
457A VAL* 1.3 68.7 + - - +
458A LEU* 3.4 34.8 - - + -
501A THR 3.8 17.0 - - - +
502A ILE* 4.0 9.4 - - + -
505A ALA* 3.2 29.8 - - + -
513A VAL* 4.5 4.9 - - + +
514A LYS 2.8 7.1 + - - +
515A ILE* 3.4 21.5 - - + -
516A TYR* 2.9 26.0 + - - -
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Residues in contact with VAL 457 (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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372A TYR* 6.4 0.2 - - + -
376A LEU* 3.9 21.5 - - + -
379A ILE* 3.9 16.4 - - + -
387A VAL* 3.9 17.9 - - + -
388A LEU 2.7 17.4 + - - +
389A VAL* 3.4 7.8 - - + -
390A PHE* 2.8 31.2 + - - -
456A LEU* 1.3 84.4 - - - +
458A LEU* 1.3 68.2 + - - +
459A ALA* 4.1 5.6 - - - +
516A TYR* 3.7 33.7 - - + +
518A CYS* 4.4 8.7 - - + -
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Residues in contact with LEU 458 (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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390A PHE* 3.9 4.3 - - + -
436A MET* 3.5 22.9 - - + -
456A LEU* 3.4 26.9 - - + +
457A VAL* 1.3 72.0 - - - +
459A ALA* 1.3 61.2 + - - +
460A GLY 3.1 8.7 + - - +
498A ILE* 3.9 17.3 - - + +
501A THR* 3.5 14.8 - - + -
502A ILE* 4.3 10.3 - - + -
515A ILE* 5.1 0.9 - - + -
516A TYR 2.8 15.0 + - - +
517A LEU* 3.7 17.9 - - + -
518A CYS* 3.0 26.9 + - - +
522A TYR* 3.2 38.0 - - + +
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Residues in contact with ALA 459 (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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372A TYR* 3.7 24.2 - - + -
376A LEU* 5.0 2.5 - - + -
389A VAL* 3.7 15.3 - - + -
390A PHE 2.8 17.4 + - - +
391A PHE* 3.7 25.9 - - + -
392A PRO* 3.2 20.6 - - - +
396A MET* 3.4 9.7 - - - +
457A VAL* 3.6 6.9 + - + -
458A LEU* 1.3 69.6 - - - +
460A GLY* 1.3 59.0 + - - +
518A CYS* 4.4 0.2 - - - -
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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