Contacts of the strand formed by residues 258 - 265 (chain C) in PDB entry 3V4P
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 LEU 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C LEU* 3.9 29.6 - - + +
194C VAL* 3.6 37.7 - - + -
203C LYS* 3.6 22.2 - - + -
204C ALA 3.2 4.2 + - - +
205C PHE* 3.1 50.6 - - + +
206C LEU 4.5 2.4 + - - +
235C VAL* 5.3 2.7 - - + -
251C PHE* 4.4 16.6 - - + -
252C SER 3.6 13.9 - - - +
253C ILE* 4.6 8.5 - - + -
257C GLU* 1.3 81.2 - - - +
259C ASN* 1.3 63.9 + - - +
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Residues in contact with ASN 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C PHE* 4.6 1.3 - - - -
208C LYS* 5.6 2.9 - - - +
251C PHE* 3.3 4.3 - - - -
252C SER* 3.0 35.0 + - - +
254C ASP* 2.8 31.6 + - - +
256C LYS* 6.1 0.2 - - - +
257C GLU* 3.4 33.5 + - - +
258C LEU* 1.3 76.4 - - - +
260C ILE* 1.3 66.8 + - - +
261C LEU 3.3 0.2 + - - -
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C PHE* 3.6 22.7 - - + -
211C GLN* 3.5 32.4 + - + +
212C VAL* 4.3 7.9 - - + -
249C TYR* 3.6 30.3 - - + -
250C ILE 3.8 4.3 - - - +
251C PHE* 3.5 21.5 - - + -
259C ASN* 1.3 74.0 - - - +
261C LEU* 1.3 63.7 + - - +
262C HIS* 3.6 27.8 - - - +
263C GLU* 4.9 2.9 - - + -
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Residues in contact with LEU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ARG* 3.2 47.3 - - + +
234C GLU* 4.2 8.1 - - + -
250C ILE* 2.5 22.0 + - + +
251C PHE 4.6 1.8 - - - +
252C SER* 3.9 18.4 - - - +
259C ASN 3.3 2.0 + - - -
260C ILE* 1.3 76.0 - - - +
262C HIS* 1.3 60.7 + - - +
315C GLY 4.6 7.5 - - - +
316C ALA* 3.6 24.8 - - + +
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Residues in contact with HIS 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ALA 4.6 0.2 - - - -
249C TYR* 3.2 5.7 - - - -
250C ILE* 2.9 39.8 + - + -
260C ILE* 3.6 10.2 - - - +
261C LEU* 1.3 82.1 + - - +
263C GLU* 1.3 82.8 + - - +
264C MET* 3.8 20.8 - - + +
316C ALA* 3.4 25.3 + - + +
317C VAL* 4.3 13.5 - - + +
318C MET* 3.6 37.0 + - + +
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLN 5.3 2.1 - - - +
242C HIS* 5.1 0.2 - - - -
247C LYS* 2.5 44.1 + - + +
248C ALA 3.6 3.8 - - - -
249C TYR* 3.4 28.0 + - + -
260C ILE* 4.9 3.6 - - + -
262C HIS* 1.3 89.6 + - - +
264C MET* 1.3 75.2 + - - +
265C LYS* 5.1 0.7 - - + +
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Residues in contact with MET 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C LYS* 3.3 4.0 - - - +
248C ALA* 2.9 64.5 + - + +
249C TYR* 4.4 1.1 - - - +
250C ILE* 4.1 25.6 - - + +
262C HIS* 3.8 20.6 - - + +
263C GLU* 1.3 84.5 - - - +
265C LYS* 1.3 61.1 + - - +
273C PHE* 3.2 10.6 - - + -
290C LEU* 4.4 12.1 - - + -
309C TYR* 3.7 52.7 - - + +
318C MET* 4.2 7.6 - - - -
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C HIS 6.0 0.2 - - - -
243C GLU* 3.6 24.5 + - - -
245C ILE* 3.7 28.1 - - + +
246C GLY 4.0 3.6 - - - +
247C LYS* 3.9 26.7 - - + +
263C GLU* 5.1 1.3 - - + +
264C MET* 1.3 75.4 - - - +
266C GLY* 1.3 73.6 + - - +
267C LYS* 5.3 1.6 - - - +
273C PHE* 3.9 11.5 - - - -
309C TYR* 3.9 8.0 + - - -
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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