Contacts of the strand formed by residues 235 - 242 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D LEU* 5.2 0.2 - - - -
173D HIS* 2.9 27.5 + - - -
175D CYS* 3.5 2.6 - - - -
197D MET* 4.4 6.7 - - - -
232D VAL* 2.9 23.1 + - - +
233D PRO 3.4 1.6 + - - -
234D GLY* 1.3 80.3 - - - +
236D CYS* 1.3 65.3 + - - -
264D MET 3.3 11.7 - - - -
265D TYR* 4.1 2.0 - - - -
266D TYR 4.3 2.0 - - - -
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Residues in contact with CYS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D CYS* 2.0 47.1 - - + -
195D VAL* 5.1 1.6 - - - -
196D SER 4.6 1.6 - - - -
197D MET* 3.7 30.1 - - - -
229D ILE* 4.0 15.5 - - + -
230D SER 3.4 6.7 - - - +
232D VAL* 3.7 6.3 - - - +
235D GLY* 1.3 74.6 - - - -
237D MET* 1.3 60.6 + - - +
238D MET 4.1 0.2 - - - -
262D ILE 3.8 0.7 - - - +
263D ILE* 3.4 3.8 - - - +
264D MET* 2.8 43.3 + - + +
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Residues in contact with MET 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ILE* 3.6 2.1 - - - -
230D SER 2.9 30.9 + - - +
232D VAL* 3.8 15.2 - - + +
236D CYS* 1.3 73.6 - - - +
238D MET* 1.3 62.4 + - - +
261D ILE* 3.7 26.7 - - + -
262D ILE 3.3 4.5 - - - +
263D ILE* 3.7 28.9 - - + +
301D VAL* 3.8 19.3 - - + -
303D PHE* 3.5 32.4 - - + -
365D CYS* 4.2 8.1 - - + -
366D PRO 4.4 6.5 - - - +
367D LEU* 3.8 26.9 - - + -
371D LEU* 4.5 2.9 - - + -
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Residues in contact with MET 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D THR* 3.5 33.9 - - - -
193D GLN* 4.1 7.2 - - + -
195D VAL* 3.7 14.6 - - + -
218D LEU* 3.6 31.9 - - + -
227D CYS* 3.9 11.7 - - + -
228D SER 3.3 12.8 - - - +
229D ILE* 4.3 5.8 - - + +
236D CYS 4.1 0.4 - - - -
237D MET* 1.3 74.7 - - - +
239D TYR* 1.3 62.7 + - - +
240D CYS* 3.8 15.0 - - - -
260D ARG 3.8 0.7 - - - +
261D ILE* 3.4 6.2 - - - +
262D ILE* 2.7 50.1 + - + +
264D MET* 3.9 15.7 - - + +
303D PHE* 4.4 2.0 - - - -
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Residues in contact with TYR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D CYS* 3.2 3.1 - - - -
228D SER 2.8 35.8 + - - -
238D MET* 1.3 72.1 - - - +
240D CYS* 1.3 74.1 + - - +
259D GLN* 2.4 40.7 + - + +
260D ARG 3.4 10.5 - - - -
261D ILE* 3.7 19.5 - - + -
275D ILE* 4.7 2.5 - - + -
287D LEU* 3.7 19.4 - - - +
289D PRO* 3.3 34.7 - - + +
303D PHE* 3.8 30.9 - - + -
305D ILE* 3.4 25.8 - - + +
363D LEU* 3.7 20.8 - - + +
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Residues in contact with CYS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ARG* 4.0 24.2 - - + -
225D LYS 3.9 3.8 - - - +
227D CYS* 2.1 47.8 - - - -
238D MET* 3.8 17.7 - - - -
239D TYR* 1.3 80.3 - - - +
241D PHE* 1.3 58.6 + - - +
259D GLN 3.7 0.3 - - - -
260D ARG* 2.8 37.9 + - + +
262D ILE* 4.1 13.5 - - + -
289D PRO* 3.9 8.7 - - - -
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Residues in contact with PHE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ARG* 3.6 3.3 - - - -
225D LYS* 2.8 63.5 + - + +
226D SER* 3.6 17.3 - - - -
240D CYS* 1.3 76.0 - - - +
242D VAL* 1.3 65.0 + - - +
243D SER* 3.8 30.3 - - - -
250D ASP* 3.7 22.4 - - - -
257D PRO* 3.7 23.3 - - + -
258D GLU 3.3 12.3 - - - +
259D GLN* 3.8 17.9 - - - +
260D ARG 4.6 0.2 - - - +
287D LEU 4.0 2.5 - - - +
288D ASN* 3.5 31.0 - - - -
289D PRO* 4.1 4.6 - - + +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ASN* 5.6 3.4 - - - +
222D VAL* 3.7 26.0 - - + -
223D ASN* 3.6 11.4 - - + +
224D ARG* 4.8 2.9 - - + -
241D PHE* 1.3 82.5 - - - +
243D SER* 1.3 64.0 + - - +
244D THR* 3.7 23.2 + - + +
257D PRO* 3.9 11.6 - - - +
258D GLU* 2.9 37.8 + - + +
260D ARG* 3.6 33.0 - - - +
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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