Contacts of the strand formed by residues 313 - 321 (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 GLY 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A SER* 3.3 16.2 - - - -
234A TYR* 3.8 14.1 - - - -
258A LEU* 4.3 5.8 - - - +
260A ASP* 2.7 41.7 + - - +
261A ILE* 4.9 0.4 - - - -
311A ALA 3.1 2.8 + - - -
312A GLN* 1.3 77.8 - - - +
314A PHE* 1.3 59.5 + - - -
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Residues in contact with PHE 314 (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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225A VAL 3.5 18.4 - - - -
226A TYR* 3.3 9.3 - - - +
227A SER* 2.9 56.8 + - - -
230A PHE* 4.1 1.6 - - - -
242A TRP* 4.2 19.7 - + - -
256A PHE* 4.8 4.0 - + - -
258A LEU* 3.4 23.3 - - - +
259A PHE* 3.9 16.6 - + + -
260A ASP 4.7 0.4 - - - +
261A ILE* 4.9 3.6 - - + -
268A VAL* 3.9 24.0 - - + -
301A LEU* 4.6 5.2 - - + -
303A PHE* 3.7 28.3 - + - -
313A GLY* 1.3 76.9 - - - +
315A ALA* 1.3 72.9 + - - +
316A VAL* 3.7 15.9 - - + -
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Residues in contact with ALA 315 (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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33A PHE* 4.3 12.8 - - + -
224A VAL* 4.2 7.0 - - + -
225A VAL 3.6 5.6 - - - -
226A TYR* 3.5 29.2 - - + -
256A PHE* 3.5 3.0 - - - -
257A PRO* 3.2 20.5 - - + +
258A LEU* 3.0 30.7 + - + +
314A PHE* 1.3 76.8 - - - +
316A VAL* 1.3 60.7 + - - +
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Residues in contact with VAL 316 (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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223A SER 3.8 1.0 - - - +
224A VAL* 3.4 4.4 - - - +
225A VAL* 2.8 55.3 + - + +
254A PHE* 3.8 30.5 - - + -
255A SER 3.4 11.9 - - - +
256A PHE* 3.7 26.9 - - + -
301A LEU* 3.7 29.6 - - + -
314A PHE* 3.7 8.7 - - + -
315A ALA* 1.3 73.2 - - - +
317A LEU* 1.3 63.6 - - - +
318A TYR* 4.0 2.0 + - + +
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Residues in contact with LEU 317 (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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30A PRO* 6.2 2.7 - - + -
33A PHE* 5.0 13.0 - - + -
222A SER* 4.1 8.1 - - - +
223A SER* 3.6 11.9 - - - +
224A VAL* 4.1 16.6 - - + +
253A HIS* 3.7 1.0 + - - +
254A PHE* 3.5 2.4 - - - -
255A SER* 2.9 48.1 + - - +
257A PRO* 4.2 12.3 - - + +
316A VAL* 1.3 74.1 - - - +
318A TYR* 1.3 76.9 + - - +
319A GLN* 4.0 29.3 - - + +
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Residues in contact with TYR 318 (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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218A TYR* 3.5 18.1 - + + +
219A SER 3.9 1.4 + - - -
220A ALA 3.0 40.6 + - - -
221A MET 3.8 4.5 - - - -
222A SER* 3.0 27.0 - - - -
223A SER* 3.1 46.8 + - - -
225A VAL* 4.6 8.3 - - + -
244A ILE* 3.7 45.3 - - + -
246A VAL* 4.4 3.1 - - + -
252A ILE* 4.1 10.8 - - + -
253A HIS 3.2 8.5 - - - +
254A PHE* 4.0 21.5 - - + -
316A VAL* 4.0 2.0 + - + -
317A LEU* 1.3 74.4 - - - +
319A GLN* 1.3 62.7 + - - +
320A ALA* 4.4 1.8 - - + -
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Residues in contact with GLN 319 (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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221A MET 3.8 3.8 - - - -
222A SER* 3.7 16.6 + - - -
252A ILE* 3.6 2.4 - - - -
253A HIS* 2.8 68.0 + - + +
255A SER* 5.3 1.9 + - - -
317A LEU* 4.0 27.8 - - + +
318A TYR* 1.3 73.9 - - - +
320A ALA* 1.3 63.0 + - - +
321A VAL* 4.1 5.4 - - + +
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Residues in contact with ALA 320 (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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221A MET* 2.8 38.7 + - - +
246A VAL* 3.7 37.7 - - + -
249A ALA* 4.1 7.9 - - + -
251A HIS 3.9 4.5 - - - -
252A ILE* 4.2 8.5 - - + -
318A TYR* 4.3 2.9 - - + -
319A GLN* 1.3 76.3 - - - +
321A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 321 (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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249A ALA* 3.3 2.0 - - - +
250A SER* 2.7 39.6 + - - +
251A HIS* 3.1 47.9 + - + +
253A HIS* 5.3 4.7 - - + +
319A GLN* 4.1 9.6 - - + +
320A ALA* 1.3 80.2 - - - +
322A LYS* 1.3 63.8 + - - +
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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