Contacts of the strand formed by residues 235 - 242 (chain A) in PDB entry 4JF7
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 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.9 0.2 - - - -
173A HIS* 2.9 21.4 + - - -
175A CYS* 3.5 1.6 - - - -
197A MET* 4.3 10.8 - - - -
232A VAL* 2.8 31.1 + - - +
233A PRO 3.3 2.4 + - - -
234A GLY* 1.3 81.4 - - - +
236A CYS* 1.3 63.9 + - - -
264A MET 3.3 11.7 - - - -
265A TYR* 4.2 1.3 - - - -
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Residues in contact with CYS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A CYS* 2.0 43.5 - - - -
195A VAL* 5.1 2.0 - - - -
196A SER 4.4 1.8 - - - -
197A MET* 3.8 30.3 - - + -
229A ILE* 3.9 17.3 - - + -
230A SER 3.3 7.2 - - - +
232A VAL* 3.7 6.1 - - - +
235A GLY* 1.3 75.0 - - - -
237A MET* 1.3 61.6 + - - +
238A MET 4.2 0.2 - - - -
262A ILE 3.8 0.2 - - - +
263A ILE* 3.4 5.4 - - - +
264A MET* 2.9 42.7 + - + +
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Residues in contact with MET 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ILE* 3.5 2.3 - - - +
230A SER 2.9 31.4 + - - +
232A VAL* 3.9 14.3 - - + +
236A CYS* 1.3 74.4 - - - +
238A MET* 1.3 62.6 + - - +
261A ILE* 3.7 26.7 - - + -
262A ILE 3.3 4.5 - - - +
263A ILE* 3.8 18.8 - - + -
301A VAL* 3.8 24.2 - - + -
303A PHE* 3.4 30.4 - - + -
365A CYS* 4.2 8.3 - - + -
366A PRO 4.0 15.7 - - - +
367A LEU* 3.7 26.9 - - + -
371A LEU* 4.5 2.0 - - + -
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Residues in contact with MET 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A THR* 3.4 30.7 - - - -
193A GLN* 4.0 6.3 - - + -
195A VAL* 3.7 15.5 - - + -
218A LEU* 3.6 31.0 - - + -
227A CYS* 3.8 16.2 - - + -
228A SER 3.4 12.3 - - - +
229A ILE* 4.1 6.1 - - + -
237A MET* 1.3 76.2 - - - +
239A TYR* 1.3 63.9 + - - +
240A CYS* 3.8 15.9 + - - -
260A ARG 3.8 0.3 - - - +
261A ILE* 3.4 6.1 - - - +
262A ILE* 2.6 51.1 + - + +
264A MET* 3.9 15.7 - - + +
303A PHE* 4.4 1.3 - - - -
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Residues in contact with TYR 239 (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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227A CYS* 3.1 2.9 - - - -
228A SER 2.9 35.1 + - - +
238A MET* 1.3 75.3 - - - +
240A CYS* 1.3 70.9 + - - +
259A GLN* 2.7 38.0 + - + +
260A ARG 3.4 10.8 - - - -
261A ILE* 3.6 19.3 - - + -
275A ILE* 4.7 1.1 - - + +
287A LEU* 3.9 11.8 - - - +
289A PRO* 3.3 36.1 - - + +
303A PHE* 3.7 33.7 - + + -
305A ILE* 3.6 27.5 - - + +
363A LEU* 3.5 23.0 - - + +
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Residues in contact with CYS 240 (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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224A ARG* 4.1 21.8 - - + -
225A LYS 3.9 6.3 - - - +
227A CYS* 2.1 49.1 - - - -
238A MET* 3.8 22.2 - - - -
239A TYR* 1.3 79.3 - - - +
241A PHE* 1.3 60.0 + - - +
260A ARG* 2.8 36.2 + - + +
262A ILE* 4.2 8.1 - - + -
289A PRO* 3.9 6.1 - - - -
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Residues in contact with PHE 241 (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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224A ARG* 3.7 2.8 - - - -
225A LYS* 2.9 55.6 + - + -
226A SER* 3.7 17.0 - - - -
240A CYS* 1.3 76.5 - - - +
242A VAL* 1.3 72.0 + - - +
243A SER* 3.7 34.1 - - - -
250A ASP* 3.9 18.6 - - - -
257A PRO* 3.6 15.3 - - + -
258A GLU 3.3 10.1 - - - +
259A GLN* 3.9 18.8 - - - +
260A ARG 4.7 0.2 - - - +
287A LEU 4.0 3.1 - - - +
288A ASN* 3.3 37.0 - - - -
289A PRO* 4.1 5.8 - - + +
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Residues in contact with VAL 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL* 3.8 24.0 - - + -
223A ASN* 3.6 13.0 - - + +
224A ARG* 4.6 4.5 - - + -
241A PHE* 1.3 85.0 - - - +
243A SER* 1.3 61.3 + - - +
244A THR* 3.8 21.5 + - + +
257A PRO* 3.7 12.5 - - - +
258A GLU* 2.8 37.1 + - + +
260A ARG* 3.7 32.8 - - - +
373D ASN* 5.6 4.0 - - - +
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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
------------------------------------------------------------
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