Contacts of the strand formed by residues 245 - 254 (chain A) in PDB entry 3ARE
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 TRP 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 4.1 27.1 + - + +
212A GLY 2.9 22.0 + - - -
213A PHE* 3.0 46.0 + - + -
214A TYR* 4.6 6.3 - + - -
216A LYS* 3.5 60.5 - - + +
237A PHE* 3.7 26.5 - - + -
238A LEU 3.7 18.6 - - - -
239A PRO* 3.7 28.5 - - + -
240A ASN* 3.4 5.6 - - - +
243A GLU 3.8 13.1 + - - -
244A THR* 1.3 83.5 - - - +
246A TYR* 1.3 59.1 + - - +
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TRP* 4.2 15.3 - + - -
209A HIS* 2.7 39.2 + - + -
210A VAL 3.4 6.7 - - - -
211A SER* 3.5 26.2 - - - +
213A PHE* 4.3 1.1 - - - -
236A ASP 4.0 0.2 - - - +
237A PHE* 3.6 3.6 - - - +
238A LEU* 2.8 68.9 + - + +
240A ASN* 3.7 11.0 - - - +
245A TRP* 1.3 73.4 - - - +
247A LEU* 1.3 72.8 + - - +
248A GLN* 3.0 26.8 + - + +
10B TYR* 4.1 22.8 - + + +
11B SER 4.3 11.2 - - - -
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Residues in contact with LEU 247 (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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210A VAL* 2.8 36.3 + - + +
213A PHE* 4.1 14.6 - - + -
218A VAL* 3.7 27.6 - - + +
220A VAL* 3.8 20.9 - - + -
234A ARG* 4.2 20.0 - - + -
235A GLY 3.4 40.4 - - - +
236A ASP 3.9 12.8 - - - -
237A PHE* 4.0 13.2 - - + +
246A TYR* 1.3 82.3 - - - +
248A GLN* 1.3 66.0 + - - +
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Residues in contact with GLN 248 (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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205A GLN* 5.1 2.1 + - - -
207A VAL* 3.6 18.7 - - + +
208A CYS 3.1 12.8 - - - +
209A HIS* 4.3 0.2 - - - -
220A VAL* 5.6 0.2 - - - -
233A HIS 4.1 0.5 - - - +
235A GLY* 3.0 31.2 + - - -
236A ASP 5.3 0.6 + - - -
238A LEU* 6.2 0.9 - - + -
246A TYR* 3.0 31.8 + - + +
247A LEU* 1.3 80.2 - - - +
249A ALA* 1.3 58.9 + - - +
250A THR* 3.6 19.5 + - + +
99B MET 3.3 29.5 + - - -
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Residues in contact with ALA 249 (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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208A CYS* 2.8 30.9 + - + +
220A VAL* 3.6 42.7 - - + +
222A TRP* 3.1 13.7 + - + +
232A THR* 4.2 13.9 - - + -
233A HIS 3.6 6.1 - - - +
234A ARG* 4.9 5.2 - - + -
248A GLN* 1.3 73.0 - - - +
250A THR* 1.3 61.2 + - - +
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Residues in contact with THR 250 (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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205A GLN* 3.8 28.5 + - - +
206A LEU 3.2 12.3 - - - +
207A VAL* 3.9 8.1 - - + -
222A TRP* 4.0 1.8 - - - -
231A GLY 3.7 1.6 - - - +
232A THR* 3.6 2.8 - - - -
233A HIS* 3.0 51.8 + - - +
248A GLN* 3.6 26.0 - - + +
249A ALA* 1.3 80.6 - - - +
251A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 251 (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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205A GLN* 3.6 3.1 - - - -
206A LEU* 2.8 41.8 + - + +
222A TRP* 3.6 41.0 - - + +
224A ARG* 6.0 0.2 - - - +
229A GLN* 3.8 26.0 - - + +
231A GLY* 3.7 30.7 - - - +
232A THR* 4.0 2.7 - - - +
250A THR* 1.3 76.1 - - - +
252A ASP* 1.3 72.1 + - - +
253A VAL* 3.7 11.8 + - + -
261A LEU* 3.9 24.0 - - + -
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Residues in contact with ASP 252 (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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198A SER* 2.9 31.2 + - - -
200A ALA* 5.4 0.7 - - - +
203A HIS* 2.8 30.9 + - - -
204A ARG 3.5 5.3 - - - -
205A GLN* 4.5 6.9 + - + +
231A GLY 4.8 2.6 + - - +
251A LEU* 1.3 81.9 - - - +
253A VAL* 1.3 64.6 + - - +
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Residues in contact with VAL 253 (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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203A HIS* 3.6 3.1 - - - +
204A ARG* 2.8 47.1 + - + +
206A LEU* 3.7 27.8 - - + -
224A ARG* 5.4 1.6 - - - +
251A LEU* 4.1 13.5 - - + -
252A ASP* 1.3 82.0 + - - +
254A GLU* 1.3 65.6 + - - +
257A GLU* 4.1 15.7 - - + +
258A GLU* 4.1 16.8 - - + -
261A LEU* 3.6 29.8 - - + -
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Residues in contact with GLU 254 (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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202A GLY 4.2 9.0 - - - +
203A HIS* 3.7 30.4 + - + +
253A VAL* 1.3 73.2 - - - +
255A ALA* 1.3 74.8 + - + +
257A GLU* 2.9 42.5 + - + +
258A GLU* 3.7 2.3 - - - +
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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