Contacts of the strand formed by residues 187 - 192 (chain B) in PDB entry 6C3P
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 ALA 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B HIS* 1.3 74.6 - - - +
188B VAL* 1.3 58.1 + - - +
198B PHE* 3.4 25.8 - - + -
199B MET 3.2 19.1 - - - +
200B LEU* 3.9 8.7 - - + -
304B TYR* 4.1 14.5 - - + -
308B GLU 3.0 5.5 + - - -
309B ILE* 3.1 7.8 - - - +
310B LEU* 2.5 35.0 + - - +
315B PHE* 4.1 3.1 - - - -
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B HIS 5.3 0.2 - - - -
187B ALA* 1.3 79.8 - - - +
189B ILE* 1.3 63.0 + - - +
198B PHE* 4.2 0.6 - - - -
199B MET* 2.8 42.6 + - + +
310B LEU* 3.1 10.1 - - + -
313B GLN* 3.3 50.7 - - + +
314B ARG* 4.0 2.7 - - - -
315B PHE* 3.5 27.9 - - + -
336B THR* 3.6 24.7 - - + -
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Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 1.3 77.4 - - - +
190B ALA* 1.3 62.2 + - - +
196B LEU* 3.6 27.1 - - + -
197B CYS 3.1 26.7 - - - +
198B PHE* 3.8 19.5 - - + +
199B MET* 4.3 0.9 - - - -
261B ILE* 4.5 5.8 - - + -
270B LEU* 5.7 2.2 - - + -
275B LEU* 4.8 0.9 - - + -
309B ILE* 3.5 23.1 - - + +
310B LEU 3.1 26.9 + - - +
311B TRP* 3.6 36.3 - - + -
312B GLY* 3.3 7.0 + - - +
313B GLN 2.9 27.0 + - - +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ILE* 1.3 78.3 - - - +
191B LEU* 1.3 64.9 + - - +
192B ARG 4.0 0.2 - - - -
195B ARG 3.6 0.2 - - - +
196B LEU* 3.3 14.3 - - - +
197B CYS* 3.0 30.7 + - - +
199B MET* 3.6 16.1 - - + +
312B GLY* 5.1 3.4 - - - -
313B GLN 3.4 14.4 - - - +
314B ARG* 3.6 18.8 - - + -
339B VAL* 6.1 3.1 - - + -
341B THR* 5.6 3.1 - - - -
229C GLU* 5.2 1.1 - - - +
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Residues in contact with LEU 191 (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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190B ALA* 1.3 79.8 - - - +
192B ARG* 1.3 61.0 + - - +
194B GLY* 4.5 6.1 - - - +
195B ARG* 3.5 24.9 - - - +
196B LEU* 3.7 19.1 - - + +
314B ARG* 5.4 1.7 - - - -
340B PRO 5.6 1.3 - - - +
341B THR* 4.2 11.9 - - - +
342B PRO* 4.1 25.6 - - + -
349B LEU* 5.6 7.6 - - + -
225C SER* 4.6 0.5 + - - -
227C GLU* 3.0 40.8 - - + +
229C GLU* 4.6 7.3 - - - +
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Residues in contact with ARG 192 (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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190B ALA 3.9 0.8 + - - -
191B LEU* 1.3 74.5 - - - +
193B HIS* 1.3 90.8 + - + +
194B GLY 3.2 0.9 - - - -
195B ARG* 2.6 38.1 + - - +
197B CYS* 3.6 18.3 - - - -
199B MET* 4.3 12.8 - - - -
256B ILE* 5.7 6.9 - - - +
258B TYR* 3.1 53.7 + - - -
260B VAL* 6.1 1.6 - - + +
225C SER* 4.3 11.8 - - - -
227C GLU* 3.3 4.2 + - - -
229C GLU* 3.2 30.4 + - - +
231C VAL* 5.3 10.5 - - - +
234C HIS* 4.6 17.9 + - - -
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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