Contacts of the strand formed by residues 205 - 213 (chain B) in PDB entry 3C7N
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 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PHE* 3.7 33.7 - + - -
199B ASP 3.3 10.5 - - - -
200B LEU* 3.6 22.7 - - + -
204B THR* 1.3 74.9 + - - +
206B ASP* 1.3 92.0 + - - +
207B VAL* 3.5 26.0 - - + -
224B GLY 4.3 1.1 - - - -
225B ASP* 3.0 39.2 + - + +
228B LEU* 3.4 20.6 + - + +
312B GLY 5.6 0.2 - - - -
313B THR* 3.5 32.3 - - - -
316B PRO* 3.7 24.5 - - + -
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Residues in contact with ASP 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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147B PRO* 4.8 4.6 - - - +
149B TYR* 3.6 35.7 + - - -
175B GLU* 5.0 5.0 - - - +
176B PRO* 6.5 0.4 - - + -
197B ILE* 3.9 2.3 - - - +
199B ASP* 2.9 45.9 + - + +
204B THR* 3.9 13.9 + - + +
205B PHE* 1.3 93.0 - - - +
207B VAL* 1.3 65.0 + - - +
208B SER* 5.0 5.0 + - - +
223B ALA 3.9 9.2 - - - +
224B GLY* 4.4 1.6 - - - -
225B ASP 5.0 0.2 + - - -
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.6 30.3 - - + -
197B ILE 3.5 2.9 - - - +
198B PHE* 4.3 6.7 - - + -
205B PHE* 3.5 31.0 - - + -
206B ASP* 1.3 75.2 - - - +
208B SER* 1.3 69.4 + - - +
222B THR* 3.6 1.9 - - - -
223B ALA* 3.0 33.8 + - + +
224B GLY* 4.4 0.6 - - - -
316B PRO* 4.0 17.9 - - + +
317B VAL* 4.0 18.6 - - + -
320B ALA* 4.0 19.7 - - + -
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA* 4.1 9.0 - - - +
149B TYR* 6.1 0.7 - - - -
176B PRO* 3.2 40.9 - - - +
195B VAL 3.8 0.3 - - - +
196B LEU* 3.4 3.8 - - - +
197B ILE* 2.9 33.5 + - - +
206B ASP* 4.1 6.7 + - - +
207B VAL* 1.3 79.2 + - - +
209B ILE* 1.3 64.8 + - - +
210B LEU* 4.2 4.5 - - - -
219B VAL* 5.9 0.2 - - - -
221B SER 3.4 8.5 - - - -
222B THR* 4.1 7.8 - - - +
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Residues in contact with ILE 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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194B ASN* 5.1 0.9 - - + +
195B VAL 3.3 8.3 - - - +
196B LEU* 3.9 21.3 - - + -
208B SER* 1.3 76.3 - - - +
210B LEU* 1.3 70.5 + - - +
219B VAL* 3.7 1.1 - - - +
220B LYS* 2.8 40.4 + - + +
221B SER* 2.8 22.6 + - - +
320B ALA* 3.7 27.8 - - + +
321B LEU* 3.7 31.2 - - + +
324B ALA* 4.6 3.1 - - + -
326B LEU* 4.3 11.0 - - + -
331B ILE* 4.0 18.6 - - + -
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Residues in contact with LEU 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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174B ASN* 5.1 0.4 - - - +
176B PRO* 3.5 38.4 - - + +
177B THR* 3.3 36.6 - - + -
180B ALA* 4.5 0.9 - - + -
193B ARG 3.4 1.1 - - - +
194B ASN* 3.4 4.7 - - - +
195B VAL* 2.8 53.5 + - + +
197B ILE* 4.4 2.9 - - + -
208B SER* 4.8 1.6 - - - -
209B ILE* 1.3 84.7 - - - +
211B THR* 1.3 61.5 + - - +
212B ILE* 4.2 0.4 - - - -
217B PHE* 3.9 18.8 - - + -
218B GLU 3.4 4.7 - - - +
219B VAL* 3.8 30.1 - - + -
220B LYS* 4.4 1.8 - - - -
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Residues in contact with THR 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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192B GLU* 3.1 32.8 + - + +
193B ARG 3.1 3.4 + - - -
194B ASN* 2.7 23.6 + - - -
210B LEU* 1.3 70.9 - - - +
212B ILE* 1.3 64.9 + - - +
213B GLU* 4.0 10.5 - - - +
216B ILE 3.4 0.9 - - - +
217B PHE* 3.8 1.0 - - - -
218B GLU* 2.7 56.4 + - + +
220B LYS* 3.7 26.4 - - + +
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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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180B ALA* 4.9 0.7 - - + -
185B LEU* 4.2 14.6 - - + +
186B ASP* 4.0 20.6 - - + +
191B ALA 4.1 2.3 - - - +
192B GLU* 3.8 1.0 - - - -
193B ARG* 2.9 46.3 + - + +
195B VAL* 4.7 10.8 - - + -
210B LEU 4.8 2.9 - - - +
211B THR* 1.3 79.6 - - - +
213B GLU* 1.3 62.0 + - - +
215B GLY* 3.7 27.1 - - - +
216B ILE 3.4 16.6 - - - +
217B PHE* 3.4 40.6 - - + -
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Residues in contact with GLU 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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191B ALA 4.5 7.2 - - - +
192B GLU* 3.4 47.7 - - + +
211B THR* 4.0 8.8 - - - +
212B ILE* 1.3 71.3 - - - +
214B ASP* 1.3 80.3 + - - +
215B GLY 3.1 0.4 - - - -
216B ILE* 3.2 22.9 + - - +
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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