Contacts of the strand formed by residues 268 - 276 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LYS* 6.3 0.4 - - + -
220B ASP* 3.1 24.8 + - + +
221B THR* 3.2 20.1 - - - +
222B LEU* 2.9 24.0 + - - +
266B PRO* 3.3 2.3 - - - +
267B GLN* 1.3 86.1 - - + +
269B ARG* 1.3 65.5 + - - +
290B LEU* 4.2 22.0 - - + +
291B TYR 3.4 8.7 - - - +
292B GLU* 4.4 22.2 - - + -
307B VAL* 5.6 5.2 - - + -
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B LEU* 3.2 39.1 - - + +
224B TRP* 3.5 42.4 - - + -
247B GLU* 3.0 27.3 + - - -
262B TRP* 3.7 21.2 - - - +
266B PRO* 5.1 3.5 + - - +
267B GLN 4.4 0.2 + - - -
268B LYS* 1.3 79.9 - - - +
270B ILE* 1.3 60.2 + - - +
271B VAL* 3.7 11.8 + - + +
289B GLY 3.9 0.2 - - - +
290B LEU* 3.4 5.7 - - - +
291B TYR* 2.9 37.5 + - + +
304B TRP* 3.3 39.0 - - + -
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 3.7 35.9 - - + -
215B HIS* 4.9 7.0 - - + +
221B THR* 3.7 23.3 - - + +
222B LEU 2.9 10.8 + - - +
223B ILE* 3.6 11.7 - - + +
224B TRP* 2.9 25.9 + - - +
269B ARG* 1.3 70.0 - - - +
271B VAL* 1.3 62.3 + - - +
272B PHE* 3.8 25.4 + - + -
287B PHE* 4.2 13.9 - - + -
289B GLY 3.9 2.9 - - - -
290B LEU* 3.7 13.7 - - + -
311B VAL* 3.7 17.5 - - + -
312B GLN 5.4 0.2 - - - +
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TRP* 3.7 21.3 - - + -
226B PRO* 3.7 29.4 - - + -
228B LEU* 5.1 1.1 - - + -
245B ILE* 4.3 12.6 - - + -
269B ARG* 4.0 9.4 - - + +
270B ILE* 1.3 74.3 - - - +
272B PHE* 1.3 69.3 + - - +
273B ALA* 4.2 2.7 - - + +
287B PHE* 3.6 6.2 - - - -
288B MET* 2.8 45.5 + - + -
289B GLY 3.0 12.9 + - - +
291B TYR* 3.6 26.0 - - + -
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Residues in contact with PHE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ILE* 3.8 24.9 - - + -
189B VAL* 4.7 4.0 - - + -
191B LEU* 4.2 13.7 - - + -
197B VAL* 3.5 38.1 - - + -
201B PHE* 4.0 5.6 - + - -
223B ILE* 4.8 0.9 - - + -
224B TRP 2.9 8.3 + - - -
225B PHE* 3.2 42.7 - + + -
270B ILE* 3.8 26.0 - - + -
271B VAL* 1.3 77.6 - - - +
273B ALA* 1.3 63.3 + - - +
274B ARG 3.8 0.2 + - - -
285B TYR* 3.7 30.2 - - + -
286B ARG 3.1 3.8 - - - +
287B PHE* 3.8 32.3 - + + -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B PRO* 3.6 8.7 - - - +
228B LEU* 3.6 37.2 - - + +
271B VAL* 4.0 2.3 - - + -
272B PHE* 1.3 73.3 - - - +
274B ARG* 1.3 63.4 + - - +
275B VAL* 3.4 12.6 + - + +
285B TYR* 3.2 4.9 - - - -
286B ARG* 2.8 32.3 + - + +
288B MET* 3.7 15.9 - - + +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B PHE 4.9 1.3 - - - +
226B PRO 3.0 18.2 + - - +
227B ARG* 3.0 53.7 - - + +
228B LEU 5.3 0.7 + - - -
229B TYR* 4.0 25.4 + - - +
272B PHE 3.8 1.4 + - - -
273B ALA* 1.3 70.3 - - - +
275B VAL* 1.3 69.9 + - - +
283B ALA* 4.0 18.0 - - + +
284B MET 3.3 8.7 - - - +
285B TYR* 3.4 35.2 + - + -
8E T 4.6 1.0 + - - -
9E A 2.8 46.3 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLU 3.7 4.3 - - - -
110B GLU 4.3 4.5 - - - +
111B ASP* 3.4 44.4 - - + +
112B ILE 4.8 3.1 - - - +
190B VAL* 4.9 3.1 - - + -
229B TYR* 6.3 0.2 - - + -
273B ALA* 4.1 17.5 - - + +
274B ARG* 1.3 83.1 - - - +
276B LYS* 1.3 62.7 + - - +
282B ARG 3.4 0.2 - - - +
283B ALA* 3.8 1.2 - - - -
284B MET* 2.8 50.9 + - + +
286B ARG* 4.2 15.5 - - + -
288B MET* 6.5 0.2 - - - -
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ALA 5.7 2.8 + - - -
109B GLU* 2.8 57.1 + - + +
110B GLU* 3.7 32.1 + - - +
111B ASP* 3.5 20.8 + - - +
275B VAL* 1.3 74.1 - - - +
277B ASP* 1.3 67.5 + - - +
278B ASN* 3.3 3.5 + - - -
281B SER* 4.7 25.2 - - - +
282B ARG 3.3 8.3 - - - +
283B ALA* 5.1 0.9 - - - +
284B MET* 4.8 0.4 - - - -
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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