Contacts of the strand formed by residues 278 - 283 (chain A) in PDB entry 5FWV
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLU* 3.8 34.1 - - + +
270A LEU 3.4 3.6 - - - +
271A LEU* 4.0 10.3 - - + -
276A HIS 4.4 5.4 - - - +
277A ARG* 1.3 83.5 + - - +
279A LEU* 1.3 63.6 + - - +
280A ALA 3.8 22.9 - - - +
281A ARG* 4.3 17.0 - - + +
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Residues in contact with LEU 279 (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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270A LEU* 2.6 23.8 + - + +
271A LEU 3.7 6.5 - - - +
272A ASP* 3.4 34.8 - - + +
277A ARG* 3.3 43.1 - - - +
278A VAL* 1.3 74.6 - - - +
280A ALA* 1.3 60.2 + - + +
292A PHE* 6.0 1.1 - - + -
294A VAL* 3.9 33.2 - - + -
296A LEU* 4.1 4.5 - - + -
299A VAL* 4.4 7.9 - - + -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL 4.5 0.2 - - - -
269A GLU* 3.2 8.8 - - - +
270A LEU* 2.8 31.7 + - + -
278A VAL* 3.5 5.7 - - - +
279A LEU* 1.3 82.8 - - + +
281A ARG* 1.3 60.0 + - - +
282A PHE* 3.8 28.7 - - + -
292A PHE* 4.2 17.0 - - + -
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Residues in contact with ARG 281 (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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267A MET* 4.0 24.9 - - + -
268A VAL 3.4 5.4 - - - +
269A GLU* 2.3 43.8 + - + +
278A VAL* 4.3 16.2 - - + +
280A ALA* 1.3 75.7 - - - +
282A PHE* 1.3 72.3 + - - +
283A HIS* 4.1 21.3 + - - +
286A SER* 3.9 10.0 + - - -
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Residues in contact with PHE 282 (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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256A PHE* 4.0 24.7 - + - -
259A PHE* 3.6 24.0 - - + -
261A ILE* 5.6 0.2 - - - +
267A MET* 3.5 2.0 - - - +
268A VAL* 2.7 50.0 + - + +
269A GLU* 5.9 0.2 - - - -
270A LEU* 5.3 4.0 - - + -
280A ALA* 3.8 20.9 - - + -
281A ARG* 1.3 82.3 - - - +
283A HIS* 1.3 60.5 + - - +
286A SER* 3.2 7.6 - - - +
287A ARG 4.4 5.2 - - - -
288A PRO* 3.7 15.9 - - + -
289A PRO* 3.5 27.4 - - + -
292A PHE* 3.4 34.8 - + - -
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Residues in contact with HIS 283 (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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259A PHE* 3.7 7.8 - - - -
261A ILE* 4.2 7.4 - - - -
264A SER* 3.1 24.6 + - - +
266A ASP 3.1 21.3 - - - +
267A MET* 4.3 4.9 - - + +
281A ARG* 4.1 24.9 - - - +
282A PHE* 1.3 70.8 - - - +
284A GLY* 1.3 66.2 + - - +
285A ARG* 3.1 17.5 - - + +
286A SER* 2.4 83.0 + - - +
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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