Contacts of the strand formed by residues 194 - 209 (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 ASP 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B PHE* 3.1 6.7 - - - -
178B SER* 2.8 35.5 + - - +
193B GLY* 1.3 73.7 - - - -
195B VAL* 1.3 79.8 + - - +
196B MET* 3.6 3.4 - - + +
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Residues in contact with VAL 195 (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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72A ASN* 5.8 7.0 - - + +
175B THR* 5.2 6.3 - - + -
176B VAL 4.0 1.3 - - - +
177B PHE* 3.4 30.5 - - + -
194B ASP* 1.3 86.1 + - - +
196B MET* 1.3 63.0 + - - +
197B GLY 5.0 2.0 - - - +
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Residues in contact with MET 196 (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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111B HIS* 5.0 6.7 - - + +
176B VAL* 2.8 18.5 + - + +
177B PHE 4.1 0.7 - - - -
178B SER* 3.9 17.0 - - - +
181B LEU* 3.5 43.7 - - + -
194B ASP* 3.6 12.1 - - + +
195B VAL* 1.3 80.6 - - - +
197B GLY* 1.3 59.7 - - - +
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Residues in contact with GLY 197 (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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175B THR* 3.5 10.5 - - - +
176B VAL* 2.6 38.3 + - - +
195B VAL* 5.0 1.4 - - - +
196B MET* 1.3 79.6 - - - +
198B GLY* 1.3 63.5 + - - +
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Residues in contact with GLY 198 (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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29B CYS* 5.1 2.5 - - - -
173B ALA* 5.8 2.7 - - - -
174B PHE 3.5 8.3 - - - -
175B THR* 4.6 1.6 - - - -
176B VAL* 4.5 1.7 - - - +
197B GLY* 1.3 76.3 - - - +
199B HIS* 1.3 63.1 + - - +
200B ALA 4.3 0.2 - - - -
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Residues in contact with HIS 199 (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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23B GLN* 3.6 11.7 - - - -
29B CYS* 3.1 40.1 - - + -
173B ALA* 3.2 6.0 - - - +
174B PHE* 2.9 47.5 + + + +
176B VAL* 3.4 21.8 - - + -
180B PHE* 5.0 0.4 - + - -
198B GLY* 1.3 75.7 + - - +
200B ALA* 1.3 61.0 + - - +
201B ILE* 3.7 13.5 - - + -
219B ASN* 2.7 37.3 + - - -
220B SER* 4.6 0.2 - - - -
221B TRP* 3.7 28.5 - + - -
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Residues in contact with ALA 200 (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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29B CYS* 3.4 27.7 - - + +
30B TRP* 3.5 34.8 - - + +
33B GLY 5.0 0.3 + - - -
76B PRO* 4.2 13.9 - - + -
171B GLU* 3.8 9.6 - - - +
172B GLY 3.2 9.0 - - - +
173B ALA* 4.1 3.8 - - + +
199B HIS* 1.3 75.5 + - - +
201B ILE* 1.3 65.3 + - - +
220B SER* 5.0 2.4 + - - -
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Residues in contact with ILE 201 (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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33B GLY* 3.9 6.9 - - - -
171B GLU* 3.4 11.1 - - - +
172B GLY* 2.8 44.5 + - - +
173B ALA* 4.2 1.6 - - - +
174B PHE* 3.8 26.0 - - + -
199B HIS* 3.7 22.7 - - + -
200B ALA* 1.3 79.5 - - - +
202B ARG* 1.3 63.3 + - - +
203B ILE* 3.9 26.2 - - + -
217B VAL* 3.6 22.2 - - + -
218B ALA 3.7 5.6 - - - +
219B ASN* 3.8 13.7 - - - +
220B SER 5.4 0.7 - - - +
231B PHE* 4.3 3.8 - - + -
242B ILE* 4.6 7.2 - - + -
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Residues in contact with ARG 202 (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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16B THR 4.2 2.8 + - - -
17B ILE* 2.9 29.1 + - - +
18B ALA 4.9 0.2 - - - -
19B GLN 2.9 28.3 + - - +
20B ILE* 4.7 1.0 - - - +
33B GLY* 3.9 8.2 - - - +
36B GLU* 3.5 43.0 + - - +
37B ALA* 3.8 12.6 - - + +
40B ASP* 2.9 26.0 + - - -
169B PRO* 4.0 11.9 - - + -
170B VAL 3.1 11.7 - - - +
201B ILE* 1.3 75.7 - - - +
203B ILE* 1.3 63.3 + - - +
204B LEU* 4.0 11.9 + - + +
217B VAL* 3.3 5.0 - - - +
218B ALA* 2.9 57.9 + - + +
230B PHE* 5.0 0.8 - - - -
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Residues in contact with ILE 203 (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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160B ILE* 5.1 5.4 - - + -
164B ILE* 3.8 20.1 - - + +
169B PRO* 3.1 5.6 - - - +
170B VAL* 2.7 49.5 + - + +
172B GLY* 4.9 1.3 - - - +
201B ILE* 3.9 20.4 - - + -
202B ARG* 1.3 75.4 - - - +
204B LEU* 1.3 62.3 + - - +
205B GLY 4.1 2.5 - - - +
215B TRP* 3.9 29.2 - - + -
216B LEU 3.6 10.8 - - - +
217B VAL* 4.7 8.1 - - + -
242B ILE* 4.4 15.9 - - + +
246B ILE* 3.8 28.9 - - + -
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Residues in contact with LEU 204 (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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6B ASP* 3.7 10.9 - - - +
7B ALA* 3.1 30.6 + - + +
8B ARG* 4.2 13.7 - - + +
17B ILE* 4.8 3.6 - - + -
164B ILE* 4.4 7.3 - - - +
169B PRO* 3.9 24.5 - - + -
202B ARG* 4.0 15.7 - - - +
203B ILE* 1.3 73.9 - - - +
205B GLY* 1.3 58.2 + - - +
216B LEU* 3.0 39.9 + - + +
218B ALA* 3.6 39.3 - - + +
230B PHE* 3.9 20.2 - - + -
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Residues in contact with GLY 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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5B PHE* 3.5 15.7 - - - -
164B ILE* 4.6 3.4 - - - +
203B ILE* 3.8 3.4 - - - +
204B LEU* 1.3 80.3 - - - +
206B TRP* 1.3 72.1 + - - +
215B TRP* 3.4 12.7 - - - -
216B LEU* 2.7 37.0 + - - +
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Residues in contact with TRP 206 (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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1B LEU* 4.5 4.9 - - + -
2B PRO* 2.7 46.2 + - + -
3B GLU 3.5 16.0 - - - -
4B SER* 3.7 2.0 - - - +
5B PHE* 3.2 63.4 + + + +
161B MET* 3.4 53.2 - - + -
164B ILE* 4.5 4.9 - - + -
165B TYR* 4.0 12.3 - - + -
205B GLY* 1.3 81.4 - - - +
207B GLY* 1.3 62.2 + - - +
214B TYR* 3.4 22.4 + - - +
215B TRP* 3.8 18.8 - + + -
216B LEU* 4.3 3.0 - - - +
235B ARG* 4.0 20.8 - - - +
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Residues in contact with GLY 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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3B GLU 3.8 14.4 - - - -
4B SER* 4.0 6.7 - - - -
206B TRP* 1.3 80.2 - - - +
208B ILE* 1.3 66.6 + - - +
214B TYR* 3.0 31.5 + - - -
235B ARG* 2.9 20.3 + - - -
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Residues in contact with ILE 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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3B GLU* 4.2 27.4 - - + +
4B SER* 4.6 3.9 + - - +
207B GLY* 1.3 81.1 - - - +
209B GLU* 1.3 58.0 + - - +
210B ASN 3.5 4.2 + - - -
211B GLY* 3.5 39.0 - - - +
212B VAL 3.4 5.2 - - - +
213B PRO* 4.2 9.9 - - + -
214B TYR* 3.3 6.8 + - - -
235B ARG* 5.0 5.8 - - - +
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Residues in contact with GLU 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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186B GLY* 3.4 22.3 + - - -
187B VAL* 3.3 27.8 - - + +
208B ILE* 1.3 71.3 - - - +
210B ASN* 1.3 84.7 + - - +
211B GLY 3.4 0.7 - - - -
212B VAL* 2.8 27.9 + - - +
214B TYR* 3.7 7.1 - - + -
232B LYS* 3.3 29.5 + - - +
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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