Contacts of the strand formed by residues 207 - 212 (chain B) in PDB entry 4A0L
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 GLN 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B PHE* 3.8 6.9 - - - -
201B ASN* 3.0 44.1 + - + +
204B ASN* 3.1 31.5 + - - +
205B THR 3.2 0.8 - - - -
206B ASN* 1.3 86.6 - - + +
208B LEU* 1.3 63.5 + - - +
219B LEU* 3.6 20.6 - - + +
220B ARG 3.3 9.2 - - - +
221B ASP* 3.8 8.4 + - - +
222B PHE* 4.9 0.7 - - - -
227B ILE* 3.4 37.0 - - + +
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Residues in contact with LEU 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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154B GLU* 5.7 0.2 - - + -
164B ALA* 4.3 5.2 - - + -
172B ILE* 4.0 24.9 - - + -
186B ILE* 5.1 2.0 - - + -
198B MET* 4.1 20.2 - - + -
199B LYS 3.5 9.4 - - - +
200B PHE* 3.5 50.0 - - + +
207B GLN* 1.3 74.0 - - - +
209B PHE* 1.3 61.0 + - - +
210B VAL* 3.5 10.6 + - + +
219B LEU* 3.5 5.0 - - - +
220B ARG* 2.7 41.0 + - + +
221B ASP 5.9 0.2 - - - -
222B PHE* 3.7 34.9 - - + -
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Residues in contact with PHE 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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197B GLY 3.9 0.2 - - - +
198B MET* 3.3 6.9 - - - -
199B LYS* 2.7 51.3 + - + +
201B ASN* 3.7 37.2 - - + -
208B LEU* 1.3 72.8 - - - +
210B VAL* 1.3 59.6 + - - +
217B THR* 6.2 0.4 - - + -
218B THR 3.5 3.6 - - - +
219B LEU* 3.7 29.6 - - + -
230B PHE* 4.0 20.4 - + - -
243B VAL* 4.1 11.9 - - + +
245B VAL* 3.8 38.6 - - + -
252B LEU* 3.7 21.5 - - + -
266B LEU* 4.2 14.4 - - + -
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Residues in contact with VAL 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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172B ILE* 3.7 33.2 - - + -
195B ILE* 4.3 10.8 - - + -
197B GLY 3.6 8.7 - - - +
198B MET* 4.5 2.0 - - + -
208B LEU* 3.7 24.2 - - + +
209B PHE* 1.3 79.0 - - - +
211B SER* 1.3 69.9 + - - +
212B SER* 4.6 7.0 - - - -
216B ALA 3.1 4.9 - - - +
217B THR* 3.3 0.8 - - - +
218B THR* 2.7 42.5 + - - +
220B ARG* 4.0 20.4 - - + +
243B VAL* 4.4 3.5 - - - +
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Residues in contact with SER 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ILE* 3.7 3.6 - - - +
196B THR* 2.6 45.8 + - - -
197B GLY* 3.0 24.6 + - - +
210B VAL* 1.3 73.4 - - - +
212B SER* 1.3 59.3 + - - +
216B ALA 3.3 4.3 - - - -
217B THR* 3.8 9.6 - - - -
240B TYR* 4.6 3.4 - - - -
242B CYS 3.6 13.6 + - - -
243B VAL* 3.6 23.8 - - - +
254B THR* 4.5 1.3 - - - -
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Residues in contact with SER 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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170B GLY* 5.0 0.9 - - - -
193B ASP* 2.5 40.0 + - - -
194B ALA 3.5 5.6 - - - -
195B ILE* 4.8 4.2 - - - +
196B THR* 4.4 0.9 - - - -
210B VAL* 4.6 11.2 - - - -
211B SER* 1.3 76.0 - - - +
213B ILE* 1.3 59.5 + - - +
214B ARG 3.5 0.2 - - - -
215B GLY* 3.7 13.9 - - - -
216B ALA* 2.7 34.1 + - - -
240B TYR 3.9 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