Contacts of the strand formed by residues 268 - 276 (chain A) in PDB entry 4PAR
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 LYS 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ASP* 3.0 35.1 + - + +
221A THR* 3.2 18.9 - - + -
222A LEU* 2.9 21.7 + - - +
266A PRO* 3.2 3.0 - - - +
267A GLN* 1.3 86.9 - - + +
269A ARG* 1.3 68.7 + - - +
290A LEU* 4.6 14.6 - - + +
291A TYR 3.5 7.0 - - - +
292A GLU* 2.8 37.4 + - + +
304A TRP* 4.6 0.2 - - - -
307A VAL* 4.1 15.8 - - - +
308A LYS* 6.1 1.0 - - - +
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Residues in contact with ARG 269 (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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222A LEU* 3.2 43.9 - - + +
224A TRP* 3.5 42.4 - - + +
247A GLU* 3.1 25.9 + - - -
258A LYS* 5.0 8.1 - - - +
262A TRP* 3.8 23.2 - - - +
266A PRO* 4.9 8.8 + - - +
268A LYS* 1.3 80.3 - - - +
270A ILE* 1.3 60.6 + - - +
271A VAL* 3.6 11.4 - - + +
290A LEU* 3.7 4.0 - - - -
291A TYR* 2.9 35.4 + - + +
304A TRP* 3.2 36.8 - - + -
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Residues in contact with ILE 270 (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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201A PHE* 3.5 34.8 - - + -
215A HIS* 5.3 2.7 - - + +
221A THR* 4.9 7.8 - - + +
222A LEU 2.9 14.1 + - - +
223A ILE* 3.5 25.8 - - + -
224A TRP* 2.9 25.1 + - - -
269A ARG* 1.3 71.6 - - - +
271A VAL* 1.3 60.9 + - - +
272A PHE* 3.5 21.3 - - + -
287A PHE* 3.9 20.2 - - + -
289A GLY 3.6 4.7 - - - +
290A LEU* 3.7 15.8 - - + +
311A VAL* 4.4 9.0 - - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TRP* 3.8 15.9 - - + -
226A PRO* 3.8 29.4 - - + -
228A LEU* 4.8 1.3 - - + -
245A ILE* 4.4 13.0 - - + -
269A ARG* 3.6 10.5 - - + +
270A ILE* 1.3 76.6 - - - +
272A PHE* 1.3 75.5 + - - +
273A ALA 4.5 1.1 - - - +
287A PHE* 3.4 4.9 - - - -
288A MET* 2.9 41.1 + - + -
289A GLY 2.9 11.1 + - - +
291A TYR* 3.5 30.5 - - + -
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Residues in contact with PHE 272 (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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183A ILE* 4.1 21.8 - - + -
189A VAL* 4.4 11.7 - - + -
191A LEU* 4.6 5.6 - - + -
197A VAL* 3.5 33.0 - - + -
201A PHE* 4.4 4.3 - + - -
224A TRP 2.9 9.5 + - - +
225A PHE* 3.2 42.5 - + + +
226A PRO* 3.5 2.8 - - - +
270A ILE* 3.5 22.4 - - + -
271A VAL* 1.3 76.5 - - - +
273A ALA* 1.3 63.1 + - - +
274A ARG 3.7 0.2 + - - -
285A TYR* 3.5 24.4 - - + -
286A ARG 3.1 3.8 - - - +
287A PHE* 3.5 50.5 - + + -
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Residues in contact with ALA 273 (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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226A PRO 3.6 6.1 - - - -
228A LEU* 3.6 28.9 - - + +
271A VAL* 4.2 1.2 - - - +
272A PHE* 1.3 72.4 - - - +
274A ARG* 1.3 64.4 + - - +
275A VAL* 3.3 11.4 + - + +
285A TYR* 3.3 3.5 - - - -
286A ARG 2.7 31.9 + - - +
288A MET* 3.7 33.5 - - + +
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Residues in contact with ARG 274 (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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109A GLU 4.4 0.5 - - - +
225A PHE 4.8 2.2 - - - +
226A PRO 3.1 18.3 + - - +
227A ARG* 3.0 53.5 - - + +
228A LEU 5.4 0.7 + - - -
229A TYR* 4.1 24.1 + - - +
272A PHE 3.7 1.8 + - - -
273A ALA* 1.3 70.5 - - - +
275A VAL* 1.3 66.3 + - - +
283A ALA* 3.8 25.2 - - + +
284A MET 3.3 6.5 - - - +
285A TYR* 3.5 35.7 + - + +
6F G 3.9 29.3 + - - +
7F A 4.5 4.9 + - - -
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Residues in contact with VAL 275 (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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109A GLU 3.8 3.6 - - - -
110A GLU 4.1 5.2 - - - +
111A ASP* 3.5 47.3 - - + +
112A ILE 4.8 2.2 - - - +
190A VAL* 4.7 3.8 - - + -
229A TYR* 6.2 0.7 - - + -
273A ALA* 4.0 19.7 - - + +
274A ARG* 1.3 81.7 - - - +
276A LYS* 1.3 62.0 + - - +
277A ASP* 6.0 0.2 - - - -
283A ALA* 4.6 1.6 - - - -
284A MET* 2.7 56.4 + - + +
286A ARG* 4.1 13.7 - - + -
288A MET* 5.1 4.5 - - + -
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Residues in contact with LYS 276 (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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109A GLU* 3.1 28.1 + - + +
110A GLU* 2.7 39.1 + - - +
111A ASP* 3.6 20.1 + - - +
275A VAL* 1.3 75.1 - - - +
277A ASP* 1.3 73.4 + - - +
278A ASN 3.5 3.6 + - - -
281A SER* 3.4 39.5 + - - +
282A ARG 3.5 7.6 - - - -
283A ALA* 4.5 1.6 - - - +
31H T 5.3 2.4 - - - -
32H T 3.8 23.4 + - - +
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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