Contacts of the strand formed by residues 249 - 256 (chain C) in PDB entry 6PSI
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 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186C PHE* 3.5 42.0 - - + -
193C LEU* 3.7 15.5 - - + -
195C ALA* 3.8 14.4 - - + +
212C ALA* 4.7 3.6 - - + -
214C THR* 4.0 19.3 - - + +
233C LEU 3.4 2.1 - - - +
234C ARG* 3.3 2.8 - - - -
235C LEU* 2.9 56.4 + - + +
238C LYS* 3.6 24.4 - - + +
247C GLY 4.2 1.0 + - - -
248C ASP* 1.3 69.4 - - - +
250C TYR* 1.3 67.3 + - - +
251C LEU* 3.6 17.3 + - + -
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Residues in contact with TYR 250 (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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379B LYS* 3.5 37.4 - - + -
187C ARG* 6.0 2.2 - - - -
189C GLU* 6.0 0.7 - - + -
192C ASP* 3.2 37.8 + - + -
193C LEU 2.9 23.5 + - - +
194C TYR* 3.2 23.1 - + + -
195C ALA 2.8 26.0 + - - -
232C LYS* 4.0 16.6 - - + -
233C LEU 3.0 17.5 - - - +
234C ARG* 3.7 27.9 + - + -
248C ASP* 3.9 13.2 + - + +
249C LEU* 1.3 70.2 - - - +
251C LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 251 (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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186C PHE* 4.9 1.1 - - + -
195C ALA* 3.4 32.5 - - + -
196C THR 4.1 10.5 - - - +
197C LEU* 3.9 14.1 - - + -
212C ALA* 3.8 21.5 - - + -
221C VAL* 4.0 4.0 - - + -
232C LYS* 3.3 6.6 - - - -
233C LEU* 3.0 61.9 + - + +
235C LEU* 3.6 28.5 - - + -
249C LEU* 3.6 18.5 + - + -
250C TYR* 1.3 72.1 - - - +
252C GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 252 (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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254A ARG* 2.9 41.4 + - - +
415B LYS* 4.6 11.5 + - - +
194C TYR* 3.0 34.6 + - + +
195C ALA 2.9 15.9 + - - +
196C THR* 3.3 23.0 + - - +
197C LEU 2.9 22.0 + - - -
230C GLY* 4.7 5.2 - - - +
231C ARG 3.7 7.9 - - - +
232C LYS* 4.8 2.9 - - - +
250C TYR 4.0 0.4 + - - -
251C LEU* 1.3 70.1 - - - +
253C VAL* 1.3 64.0 + - - +
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Residues in contact with VAL 253 (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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254A ARG* 3.5 7.6 + - - -
242B TRP* 3.4 31.9 - - + -
197C LEU* 4.0 4.7 - - - -
199C VAL* 4.2 11.9 - - + -
227C THR* 3.6 7.9 - - + -
228C GLN 3.6 15.5 - - - +
229C ALA* 3.3 2.8 - - - +
230C GLY 3.0 22.3 + - - -
231C ARG* 3.0 24.5 + - + +
233C LEU* 3.5 14.8 - - + -
252C GLU* 1.3 72.6 - - - +
254C ARG* 1.3 64.6 + - - +
255C ILE* 3.6 29.4 - - + -
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Residues in contact with ARG 254 (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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228A GLN* 5.3 1.8 + - - -
229A ALA* 3.3 30.9 + - + -
230A GLY* 4.4 15.2 - - - +
254A ARG* 3.8 24.2 - - - +
284B GLY* 4.4 0.4 - - - -
285B ASN* 3.1 46.7 + - - +
196C THR* 3.7 16.9 - - + +
197C LEU 3.1 10.5 + - - +
198C ASP* 2.9 30.3 + - - +
199C VAL* 2.9 32.4 + - - +
229C ALA* 4.0 3.6 - - - -
253C VAL* 1.3 73.2 - - - +
255C ILE* 1.3 62.7 + - - +
256C THR* 3.6 10.0 + - + +
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Residues in contact with ILE 255 (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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229A ALA* 3.0 20.6 - - - +
255A ILE* 3.0 37.7 - - + +
256A THR* 4.7 1.3 - - - +
257A ILE* 4.0 11.2 - - + -
199C VAL* 3.4 4.3 - - + +
201C ALA* 3.6 31.0 - - + -
204C ALA* 3.5 18.8 - - + -
227C THR 3.1 24.9 - - - +
228C GLN* 4.0 0.9 - - - -
229C ALA* 3.3 29.6 - - - +
253C VAL* 3.6 20.9 - - + -
254C ARG* 1.3 71.8 - - - +
256C THR* 1.3 57.5 + - - +
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Residues in contact with THR 256 (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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228A GLN* 3.2 32.4 + - - +
229A ALA 4.5 1.3 - - - -
255A ILE* 4.1 5.6 - - - -
198C ASP* 3.4 36.3 + - - +
199C VAL 3.0 18.3 + - - +
200C PRO* 3.1 9.7 - - + +
201C ALA 2.9 23.2 + - - -
254C ARG* 3.6 23.3 - - - +
255C ILE* 1.3 74.7 - - - +
257C ILE* 1.3 65.2 + - - +
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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