Contacts of the strand formed by residues 432 - 436 (chain B) in PDB entry 3V5L
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 CYS 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 4.1 9.6 - - - -
365B PHE* 4.8 4.5 - - - -
390B ILE* 3.6 23.1 - - + -
391B LYS 3.3 16.6 - - - +
392B THR* 3.7 17.9 - - + -
403B PHE* 3.9 2.0 - - - -
424B VAL* 3.7 4.9 - - - +
425B CYS* 2.8 63.7 + - - +
430B PRO 4.9 2.5 - - - -
431B ILE* 1.3 74.8 - - - +
433B LEU* 1.3 63.5 + - - +
434B VAL* 5.0 1.1 - - - -
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA 3.6 2.8 - - - +
390B ILE* 3.6 4.2 - - - +
391B LYS* 2.9 36.6 + - + +
403B PHE* 3.6 56.1 - - + +
406B GLU* 5.3 4.0 - - + +
407B ALA* 3.8 24.7 - - + +
410B MET* 4.6 6.7 - - + -
421B LEU* 4.1 6.3 - - + -
423B GLY 3.9 2.9 - - - -
424B VAL* 3.8 20.2 - - + -
432B CYS* 1.3 71.9 - - - +
434B VAL* 1.3 60.3 + - - +
435B PHE* 3.6 36.3 + - + -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ILE* 3.9 22.7 - - + -
363B LEU* 3.8 41.3 - - + -
382B TRP* 4.6 1.8 - - + -
388B VAL* 3.8 32.3 - - + -
389B ALA 4.1 1.6 - - - -
390B ILE* 4.9 3.4 - - + +
421B LEU* 3.5 3.7 - - - -
422B TYR* 2.7 43.5 + - + -
423B GLY 2.8 22.7 + - - +
425B CYS 4.7 6.7 - - - +
432B CYS* 4.7 2.2 - - - +
433B LEU* 1.3 73.4 - - - +
435B PHE* 1.3 54.4 + - - +
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B VAL* 3.4 11.1 - - - +
389B ALA 3.0 40.8 + - - +
391B LYS* 3.8 28.3 - - + -
410B MET* 3.9 14.8 - - + -
419B VAL* 4.1 22.4 - - + -
420B GLN 3.7 8.5 - - - -
421B LEU* 3.7 28.0 - - + +
422B TYR* 4.2 3.1 - - - -
433B LEU* 3.7 39.3 - - + -
434B VAL* 1.3 73.9 - - - +
436B GLU* 1.4 61.1 + - - +
499B SER* 4.6 3.6 - - - -
500B ASP* 4.8 8.5 - - - -
701B 0G1 3.7 31.0 - + + -
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Residues in contact with GLU 436 (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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389B ALA* 4.0 0.5 - - - +
419B VAL* 3.7 7.7 - - + +
420B GLN* 2.9 55.2 + - + +
422B TYR* 4.0 22.4 - - + +
435B PHE* 1.4 74.9 - - - +
437B PHE* 1.3 61.9 + - - +
438B MET* 4.2 14.0 - - - +
497B LYS* 2.8 38.6 + - - +
701B 0G1 3.0 20.6 + - - -
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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