Contacts of the strand formed by residues 212 - 219 (chain B) in PDB entry 1CPJ
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 VAL 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B VAL* 3.8 28.0 - - + +
208B ILE* 3.4 0.8 - - - -
209B GLU* 2.8 42.5 + - - +
210B ASN* 3.9 8.1 - - + +
211B GLY* 1.3 73.6 - - - +
213B PRO* 1.3 63.3 - - - +
214B TYR* 3.6 2.8 + - - -
234B LEU* 3.6 25.6 - - + -
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Residues in contact with PRO 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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157B GLU* 5.3 0.9 - - - +
207B GLY 3.4 8.3 - - - +
208B ILE* 4.2 10.3 - - + -
211B GLY 3.1 10.9 - - - +
212B VAL* 1.3 82.3 - - - +
214B TYR* 1.3 52.2 + - - +
234B LEU* 3.1 23.1 - - + +
235B ARG* 2.8 67.7 + - - +
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Residues in contact with TYR 214 (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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187B VAL* 3.7 27.4 - - + -
206B TRP* 3.4 7.7 + - - +
207B GLY* 3.0 40.9 + - - -
208B ILE 3.3 18.3 + - - -
209B GLU* 3.7 23.8 - - + -
213B PRO* 1.3 74.8 - - - +
215B TRP* 1.3 78.3 + - - +
216B LEU* 4.0 13.0 - - + +
232B LYS* 3.5 36.5 - - + +
233B ILE 3.1 13.7 - - - +
235B ARG* 3.1 22.7 + - - +
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Residues in contact with TRP 215 (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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157B GLU* 4.2 10.3 - - + -
160B ILE* 3.7 27.1 - - + -
161B MET* 3.5 30.7 - - + -
164B ILE* 4.1 18.8 - - + -
203B ILE* 3.9 18.6 - - + -
205B GLY 3.4 19.1 - - - +
206B TRP* 3.8 18.4 - + + -
214B TYR* 1.3 76.7 - - - +
216B LEU* 1.3 61.1 + - - +
217B VAL* 3.6 8.7 + - + +
232B LYS* 3.3 8.3 - - - -
233B ILE* 2.7 36.0 + - + +
234B LEU 3.9 11.4 - - - -
235B ARG* 3.1 29.5 - - + +
242B ILE* 3.9 18.3 + - + +
243B GLU* 3.1 30.4 + - + +
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Residues in contact with LEU 216 (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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5B PHE 4.7 2.2 - - - +
6B ASP* 3.5 36.6 - - + +
8B ARG* 4.1 9.4 - - - +
203B ILE* 3.6 5.2 - - - +
204B LEU* 3.0 46.2 + - + -
205B GLY* 2.7 28.6 + - - +
206B TRP 4.4 1.1 - - - +
214B TYR* 3.9 12.8 - - + +
215B TRP* 1.3 70.1 - - - +
217B VAL* 1.3 62.9 + - - +
227B ASP* 6.0 1.1 - - - +
230B PHE* 4.1 24.7 - - + -
231B PHE 4.0 4.5 - - - +
232B LYS* 5.0 11.2 - - + -
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Residues in contact with VAL 217 (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 ILE* 3.6 24.2 - - + -
202B ARG 3.3 11.4 - - - +
203B ILE* 4.7 7.6 - - + -
204B LEU* 4.3 2.9 - - - -
215B TRP* 3.6 18.6 - - + +
216B LEU* 1.3 81.9 - - - +
218B ALA* 1.3 63.8 + - - +
219B ASN 3.5 0.3 + - - -
230B PHE* 3.1 7.8 - - - +
231B PHE* 2.8 83.7 + - + +
233B ILE* 4.2 10.8 - - + -
242B ILE* 5.3 3.1 - - + -
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Residues in contact with ALA 218 (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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20B ILE* 3.9 13.5 - - + -
36B GLU* 4.7 3.6 - - - +
201B ILE* 3.7 3.5 - - - +
202B ARG* 2.9 70.2 + - + +
204B LEU* 3.6 12.7 - - + +
217B VAL* 1.3 76.4 - - - +
219B ASN* 1.3 61.9 + - - +
229B GLY 4.2 3.8 - - - -
230B PHE* 4.3 2.7 - - + -
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Residues in contact with ASN 219 (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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20B ILE* 3.6 22.5 - - - +
36B GLU* 4.7 4.8 - - - +
180B PHE* 3.9 5.4 - - - -
199B HIS* 2.7 34.8 + - - -
200B ALA 5.1 0.2 + - - -
201B ILE* 3.8 6.4 - - - +
217B VAL 3.5 3.8 + - - -
218B ALA* 1.3 76.8 - - - +
220B SER* 1.3 67.8 + - - +
221B TRP* 3.2 38.4 + - - +
225B TRP* 3.5 26.9 - - + -
229B GLY 3.2 17.4 + - - +
231B PHE* 4.3 10.6 - - + -
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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