Contacts of the strand formed by residues 241 - 250 (chain A) in PDB entry 2AV7
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 PHE 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASP* 3.9 34.8 - - + -
207A SER* 3.1 23.9 + - - -
208A PHE* 3.0 44.9 + - + +
209A TYR* 4.1 4.7 - + - -
210A PRO 4.4 0.7 - - - -
211A ALA* 3.8 25.1 - - + -
233A THR* 3.9 8.5 - - + -
234A ARG 3.4 18.4 - - - +
235A PRO* 3.8 23.6 - - + -
236A ALA 4.4 0.2 - - - +
239A GLY 3.9 15.9 - - - -
240A THR* 1.3 77.1 - - - +
242A GLN* 1.3 63.5 + - - +
701A GOL 4.9 2.7 - - - -
716B GOL 4.0 19.5 - - - -
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Residues in contact with GLN 242 (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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204A TRP* 5.4 0.4 - - + -
205A ALA 3.3 7.9 - - - -
206A LEU* 3.6 25.5 - - + +
207A SER 4.7 2.0 - - - +
208A PHE* 3.7 2.7 - - - -
232A GLU 4.3 0.2 - - - +
233A THR* 3.4 2.6 - - - +
234A ARG* 2.8 76.1 + - + +
236A ALA* 3.5 21.1 - - + +
241A PHE* 1.3 80.3 - - - +
243A LYS* 1.3 63.8 + - - +
10B TYR* 3.3 10.6 - - - -
11B SER 3.5 10.1 + - - -
12B ARG* 3.1 26.3 + - - +
706B GOL 3.8 4.0 + - - -
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Residues in contact with LYS 243 (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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204A TRP* 3.6 6.0 - - - -
205A ALA 2.7 37.5 + - - +
208A PHE* 4.1 11.0 - - + -
213A ILE* 3.7 21.5 - - + -
215A LEU* 3.8 23.5 - - + +
230A LEU* 4.0 25.3 - - - +
231A VAL* 2.9 35.5 + - - +
232A GLU* 4.1 1.8 - - - +
233A THR* 3.0 36.9 + - - +
234A ARG* 5.6 1.1 - - - +
242A GLN* 1.3 75.6 - - - +
244A TRP* 1.3 64.5 + - - +
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Residues in contact with TRP 244 (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 ARG* 3.4 44.1 - - + +
203A CYS 3.3 12.3 - - - +
204A TRP* 3.3 39.1 - + + -
215A LEU* 3.7 3.8 - - - -
229A GLU* 3.6 44.2 - - + -
230A LEU* 3.9 5.4 - - - +
231A VAL* 3.4 58.9 + - + +
234A ARG* 4.2 4.5 - - - -
243A LYS* 1.3 79.1 - - - +
245A ALA* 1.3 65.3 + - - +
246A ALA* 3.6 21.5 - - + -
99B MET* 4.3 8.0 - - + +
707B GOL 3.3 30.4 + - - -
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Residues in contact with ALA 245 (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 CYS* 2.7 38.3 + - + +
215A LEU* 4.0 20.9 - - + +
217A TRP* 2.8 28.0 + - + +
228A THR* 4.1 4.7 - - + -
229A GLU 3.3 7.2 - - - +
230A LEU* 3.7 20.4 - - + -
244A TRP* 1.3 76.2 - - - +
246A ALA* 1.4 54.6 + - - +
259A CYS* 5.6 0.4 - - - -
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Residues in contact with ALA 246 (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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200A THR* 3.9 20.2 - - + -
201A LEU 3.2 11.0 - - - +
202A ARG* 3.9 11.9 - - + +
217A TRP* 3.8 1.3 - - - +
227A ASP 4.1 0.2 - - - +
228A THR* 3.4 6.1 - - - -
229A GLU* 2.7 42.7 + - + +
244A TRP* 3.6 21.3 - - + -
245A ALA* 1.4 72.6 - - - +
247A VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 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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200A THR* 3.5 3.5 - - - -
201A LEU* 2.8 37.5 + - + +
217A TRP* 3.7 39.9 - - + -
224A GLN* 4.6 6.7 - - + +
227A ASP 3.5 19.5 - - - +
228A THR* 3.6 14.8 - - - +
246A ALA* 1.3 79.0 - - - +
248A VAL* 1.3 64.8 + - - +
249A VAL* 3.8 8.6 + - + -
257A TYR* 3.7 29.8 - - + -
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Residues in contact with VAL 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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194A VAL* 5.1 5.2 - - + -
198A GLU* 3.6 42.0 - - + +
199A ALA 3.4 5.8 - - - +
200A THR* 4.1 18.2 - - + +
227A ASP 4.8 2.8 + - - -
247A VAL* 1.3 75.0 - - - +
249A VAL* 1.3 61.8 + - - +
250A PRO* 3.5 10.3 - - + +
257A TYR* 3.5 12.3 + - - -
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Residues in contact with VAL 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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191A HIS* 6.1 0.2 - - - +
198A GLU* 3.2 2.2 - - - -
199A ALA* 2.7 42.5 + - + +
201A LEU* 3.8 27.4 - - + -
247A VAL* 3.9 14.1 - - + +
248A VAL* 1.3 77.1 - - - +
250A PRO* 1.3 74.9 - - - +
251A SER* 4.6 0.2 - - - -
253A GLN 3.7 5.8 - - - -
254A GLU* 3.6 40.2 - - + +
257A TYR* 3.7 24.2 - - + -
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Residues in contact with PRO 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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197A HIS* 3.5 10.3 - - - +
198A GLU* 4.0 7.6 - - + +
219A ARG* 5.9 2.5 - - - +
248A VAL* 3.5 10.3 - - + +
249A VAL* 1.3 92.2 - - + +
251A SER* 1.3 67.2 + - - +
252A GLY 3.5 0.2 + - - -
253A GLN* 3.1 48.1 + - - +
254A GLU* 4.7 0.5 - - - +
257A TYR* 3.7 13.5 - - - +
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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