Contacts of the strand formed by residues 187 - 192 (chain B) in PDB entry 6CMO
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 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B TYR* 5.3 1.2 + - - -
147B SER* 3.5 15.2 + - - -
160B SER* 3.7 21.5 - - - -
161B SER 3.9 12.4 + - - +
164B THR* 3.9 27.8 - - - +
165B THR 4.2 7.4 - - - +
166B CYS* 4.4 2.9 - - - -
183B HIS* 4.2 13.9 - - + -
185B GLY 4.5 1.6 - - - +
186B ASP* 1.3 88.9 + - - +
188B MET* 1.3 59.4 + - - +
189B SER 3.7 12.6 - - - +
201B SER* 3.3 28.0 - - - +
202B GLY 3.4 11.7 - - - +
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Residues in contact with MET 188 (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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209A LYS* 4.3 26.2 - - + -
210A LYS* 3.7 32.8 + - + +
145B TYR* 4.5 0.9 - - - -
147B SER* 3.3 20.8 + - - -
148B CYS* 5.2 0.3 - - - +
186B ASP* 3.6 30.3 + - + +
187B VAL* 1.3 73.7 - - - +
189B SER* 1.3 63.4 + - - +
202B GLY 3.4 8.0 + - - +
203B ALA* 4.3 1.1 - - - -
204B CYS* 3.7 32.5 - - + +
228B ASP* 5.1 8.1 - - + +
229B ILE 3.3 26.9 - - - +
230B ASN* 4.5 9.3 - - - +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 4.0 4.4 + - - -
148B CYS* 4.6 8.5 - - - -
160B SER* 4.9 0.9 - - - -
187B VAL* 3.7 17.0 - - - +
188B MET* 1.3 79.0 - - - +
190B LEU* 1.3 65.8 + - - +
202B GLY* 3.7 18.3 + - - -
229B ILE* 4.7 3.3 + - - +
230B ASN 3.3 26.1 + - - -
231B ALA* 4.6 2.5 - - - -
232B ILE* 3.4 26.8 - - - +
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Residues in contact with LEU 190 (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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148B CYS* 4.3 24.0 - - + +
150B ARG* 3.5 37.7 + - + +
158B VAL* 3.7 33.9 - - + +
160B SER* 3.5 23.6 - - - +
166B CYS* 5.0 0.9 - - - -
189B SER* 1.3 80.3 + - - +
191B SER* 1.3 67.8 + - - +
192B LEU* 5.8 2.0 - - + -
199B PHE* 3.6 27.4 - - + -
200B VAL 3.5 21.1 - - - +
201B SER* 4.6 6.1 - - - -
232B ILE* 4.9 5.5 - - - +
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Residues in contact with SER 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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150B ARG* 4.3 10.5 - - - +
190B LEU* 1.3 80.7 - - - +
192B LEU* 1.3 64.3 + - - +
199B PHE* 3.4 4.3 - - - +
200B VAL 3.0 31.2 + - - +
232B ILE* 3.7 35.6 + - - +
233B CYS* 4.4 0.7 - - - -
234B PHE* 3.2 26.1 + - - -
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Residues in contact with LEU 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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150B ARG* 3.8 33.3 - - + +
151B PHE 4.0 17.5 - - - +
152B LEU* 4.0 22.2 - - + +
158B VAL* 5.5 5.6 - - + -
190B LEU* 5.8 2.0 - - + -
191B SER* 1.3 76.5 + - - +
193B ALA* 1.3 85.8 + - - +
194B PRO* 3.9 2.2 - - + +
196B THR* 4.6 18.6 - - + -
198B LEU 3.7 6.1 - - - +
199B PHE* 3.7 17.0 - - + -
234B PHE* 3.6 12.2 - - - +
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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