Contacts of the strand formed by residues 259 - 264 (chain C) in PDB entry 3Q2K
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 259 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C PHE* 3.7 14.7 + - - -
256C GLY 2.9 29.7 + - - +
258C LYS* 1.3 78.9 - - - +
260C THR* 1.3 65.3 + - - -
275C LYS 3.3 8.7 - - - -
276C PHE* 3.4 18.6 - - - -
244D TYR* 4.0 2.8 - - - -
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Residues in contact with THR 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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150C PHE* 4.1 0.6 - - - -
254C ILE 3.6 5.6 - - - -
255C LEU* 3.7 22.1 - - + +
256C GLY 4.9 0.2 + - - -
259C GLY* 1.3 75.9 + - - -
261C VAL* 1.3 69.4 + - - +
262C ARG* 6.0 0.2 - - + -
273C GLU* 4.5 7.2 - - + -
274C TRP* 3.4 2.4 - - - -
275C LYS* 2.7 54.7 + - + -
276C PHE* 4.5 0.4 - - - -
243D THR* 4.2 0.9 - - - +
244D TYR 2.8 31.3 + - - +
248D LEU* 4.1 20.4 - - + -
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 3.5 31.9 - - + -
150C PHE* 3.7 14.8 - - + -
252C ILE 4.0 0.4 - - - +
253C THR* 3.2 5.0 - - - +
254C ILE* 2.8 42.0 + - + +
260C THR* 1.3 85.7 - - - +
262C ARG* 1.3 65.0 + - - +
263C VAL* 4.1 11.0 - - + -
271C ILE* 5.4 0.4 - - + -
273C GLU 3.5 4.5 - - - +
274C TRP* 3.4 32.1 - - + -
276C PHE* 3.6 23.1 - - + -
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Residues in contact with ARG 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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159C ASN* 4.7 4.0 - - - +
249C GLU* 3.1 25.7 + - - -
251C SER* 4.6 7.1 + - - -
252C ILE 3.4 4.9 - - - +
253C THR* 3.5 28.1 + - + +
260C THR* 6.0 0.7 - - + -
261C VAL* 1.3 76.8 - - - +
263C VAL* 1.3 71.4 + - - +
264C GLY* 4.4 4.1 - - - +
271C ILE* 3.6 4.7 - - - +
272C ASP* 2.9 40.1 + - + +
273C GLU* 3.1 30.6 + - + +
159D ASN* 4.5 6.9 - - - +
161D PHE* 5.2 0.4 - - - -
248D LEU* 6.1 5.6 - - + +
249D GLU* 3.0 33.1 + - - -
262D ARG* 3.0 25.6 - - - +
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Residues in contact with VAL 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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137C THR* 4.0 17.5 - - - +
138C LEU* 4.4 5.8 - - + -
141C VAL* 3.8 29.2 - - + -
251C SER* 3.0 8.0 - - - -
252C ILE* 2.7 55.7 + - + +
261C VAL* 4.1 5.4 - - + -
262C ARG* 1.3 77.4 - - - +
264C GLY* 1.3 60.2 + - - +
268C VAL* 3.7 34.5 - - + +
270C ARG 3.8 8.1 - - - +
271C ILE* 4.2 8.3 - - + -
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Residues in contact with GLY 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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249C GLU* 5.5 1.6 - - - -
250C GLY 4.0 1.6 - - - -
251C SER* 3.9 12.6 - - - -
262C ARG* 3.9 4.6 - - - +
263C VAL* 1.3 72.8 - - - +
265C GLY* 1.3 62.6 + - - -
268C VAL* 3.4 4.5 - - - -
269C ASN 3.0 25.1 + - - -
270C ARG 2.9 20.5 + - - -
272C ASP* 3.8 15.5 + - - -
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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