Contacts of the strand formed by residues 204 - 213 (chain B) in PDB entry 2ANL
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 THR 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLU* 3.1 27.3 - - - +
178A TYR* 3.8 2.5 - - - -
201B PHE* 3.0 30.1 + - + +
203B LYS* 1.3 78.5 - - - +
205B SER* 1.3 61.7 + - - +
226B PHE* 3.3 18.7 + - + +
229B LYS* 3.5 25.2 - - - +
230B PHE* 3.4 39.9 - - + +
233B ASP* 4.6 0.7 - - - +
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Residues in contact with SER 205 (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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173A ILE* 5.6 9.3 - - - +
178A TYR* 4.2 3.2 + - - -
182A LEU* 4.1 22.6 - - - +
184A TYR* 4.4 12.8 + - - -
317A LYS* 5.2 2.1 + - - -
199B VAL 2.2 30.3 + - - -
200B ASN* 2.3 27.3 + - - -
203B LYS 3.6 2.7 + - - -
204B THR* 1.3 77.0 + - - +
206B MET* 1.3 60.1 + - - +
226B PHE* 3.6 8.7 - - - -
229B LYS* 5.0 7.6 + - - -
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Residues in contact with MET 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TYR* 4.4 2.9 - - - -
317A LYS* 4.4 17.0 - - - +
198B ASP* 4.2 0.2 - - - -
199B VAL* 3.1 29.8 + - + +
205B SER* 1.3 79.7 + - - +
207B GLU* 1.3 75.4 + - - +
208B LYS 4.0 1.1 + - - +
209B ALA* 4.1 17.3 + - + -
223B PRO* 5.6 2.0 - - - -
226B PHE* 4.0 20.8 - - + -
296B LYS* 3.6 15.5 - - + +
297B ASN* 3.4 35.0 - - + -
299B PHE* 4.8 10.8 - - + -
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Residues in contact with GLU 207 (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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184A TYR* 2.5 64.2 + - + +
185A GLU 5.2 0.2 - - - -
186A LYS* 5.2 9.2 + - - +
317A LYS* 3.3 53.3 - - + +
319A SER* 2.9 17.2 + - - -
198B ASP* 2.6 31.2 - - - +
206B MET* 1.3 82.2 - - - +
208B LYS* 1.3 76.9 + - + +
209B ALA 3.3 2.9 + - - -
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Residues in contact with LYS 208 (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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186A LYS* 4.2 29.2 - - - +
317A LYS* 5.4 11.9 - - + +
196B ASP* 4.0 31.7 + - + +
197B LEU 3.8 8.4 + - - +
198B ASP* 2.6 17.2 + - - -
206B MET* 5.0 1.1 - - - +
207B GLU* 1.3 87.0 - - + +
209B ALA* 1.3 67.7 + - - +
297B ASN* 4.9 7.3 + - - +
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Residues in contact with ALA 209 (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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196B ASP* 3.6 8.5 - - - +
197B LEU 2.9 31.5 + - - +
199B VAL* 4.7 8.5 - - + -
206B MET* 4.1 20.2 - - + -
207B GLU 3.3 1.5 - - - -
208B LYS* 1.3 83.7 - - - +
210B ASN* 1.3 61.5 + - - +
211B VAL* 3.9 3.8 - - + -
297B ASN* 3.5 17.7 - - - +
299B PHE* 4.4 19.7 - - + -
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Residues in contact with ASN 210 (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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188B ASN* 3.3 26.1 - - - +
189B HIS* 5.6 0.9 + - - -
194B GLN* 3.1 38.6 + - - +
195B VAL 4.0 1.3 - - - -
196B ASP* 5.2 1.3 - - - +
209B ALA* 1.3 72.9 - - - +
211B VAL* 1.3 66.1 + - - +
212B ILE* 3.9 1.8 - - - +
295B ASP* 4.8 3.6 - - - +
297B ASN* 2.5 31.2 + - - +
298B THR* 3.1 17.9 + - - +
299B PHE 2.8 27.1 + - - +
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Residues in contact with VAL 211 (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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193B TRP 3.9 0.3 - - - +
194B GLN* 3.3 0.2 - - - -
195B VAL* 3.0 41.8 + - + +
197B LEU* 4.3 26.0 - - + -
199B VAL* 4.4 14.6 - - + -
209B ALA* 4.8 2.5 - - + -
210B ASN* 1.3 79.0 - - - +
212B ILE* 1.3 76.5 + - - +
213B VAL* 4.7 4.0 - - + -
259B PHE* 4.6 4.3 - - + -
299B PHE* 3.7 31.6 - - + +
301B LEU* 4.1 24.2 - - + -
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Residues in contact with ILE 212 (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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192B PHE* 3.7 38.4 - - + -
193B TRP 3.8 8.1 - - - +
194B GLN* 3.9 11.0 - - + +
210B ASN* 3.9 14.1 - - - +
211B VAL* 1.3 90.2 - - - +
213B VAL* 1.3 67.5 + - - +
214B ASP* 3.7 3.3 + - + +
298B THR* 4.5 11.0 - - + -
299B PHE 3.3 18.6 + - - +
300B ILE* 4.1 21.8 - - + -
301B LEU* 2.4 36.2 + - - +
3152B JE2 4.8 5.6 - - + -
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Residues in contact with VAL 213 (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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35B THR* 2.5 30.6 + - - +
193B TRP* 3.7 19.3 + - - +
195B VAL* 5.5 2.9 - - + -
211B VAL* 4.7 8.1 - - + +
212B ILE* 1.3 88.8 - - - +
214B ASP* 1.3 54.0 + - - +
301B LEU* 3.4 15.9 - - + +
305B PHE* 5.1 5.4 - - + -
306B MET* 4.6 10.8 - - - -
311B THR* 4.9 6.5 - - + -
313B PHE* 3.8 31.2 - - + -
320B ILE* 4.1 17.7 - - + -
322B PHE* 5.0 9.2 - - + -
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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