Contacts of the strand formed by residues 185 - 190 (chain B) in PDB entry 4CY1
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 LEU 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B PHE* 3.3 9.7 - - - -
180B ASN* 3.0 50.5 + - - +
184B SER* 1.3 92.0 - - - +
186B ILE* 1.3 63.0 + - - +
197B ILE* 4.0 17.3 - - + -
198B TRP 3.3 8.3 - - - +
199B ASP* 4.4 2.7 - - - +
200B THR* 3.7 0.9 - - - -
206B LEU* 3.5 32.3 - - + -
222B PHE* 3.9 11.2 - - + -
243B TYR* 4.1 23.8 - - + +
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Residues in contact with ILE 186 (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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145B VAL* 4.0 20.2 - - + -
153B VAL* 4.8 5.2 - - + -
155B ILE* 3.7 36.1 - - + -
167B LEU* 5.1 2.7 - - + -
177B VAL* 4.7 3.1 - - + -
178B HIS 3.3 9.4 - - - +
179B PHE* 3.4 38.4 - - + -
185B LEU* 1.3 73.2 - - - +
187B VAL* 1.3 74.4 + - - +
188B SER* 5.1 0.4 - - - -
197B ILE* 3.3 4.2 - - - +
198B TRP* 2.7 57.7 + - + -
200B THR* 3.6 11.9 - - - +
222B PHE* 4.0 3.1 - - - -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA 3.9 0.2 - - - +
177B VAL* 3.3 5.2 - - - -
178B HIS* 2.9 46.7 + - + +
186B ILE* 1.3 76.7 - - - +
188B SER* 1.3 66.8 + - - +
195B CYS* 4.8 2.2 - - + -
196B ARG 3.3 6.7 - - - +
197B ILE* 3.6 22.9 - - + -
220B VAL* 3.8 31.0 - - + +
221B LYS* 4.2 2.0 - - - -
222B PHE* 3.6 36.7 - - + +
229B ILE* 4.2 10.8 - - + -
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Residues in contact with SER 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.9 21.0 - - - +
170B HIS* 2.8 26.8 + - - -
174B VAL* 4.4 0.7 - - - -
176B ALA 3.3 9.9 - - - -
177B VAL* 4.2 2.9 - - - -
186B ILE* 5.1 0.7 - - - -
187B VAL* 1.3 75.0 - - - +
189B SER* 1.3 60.8 + - - +
195B CYS* 3.2 6.1 - - - +
196B ARG* 2.9 33.1 + - - +
198B TRP* 2.9 28.4 + - - -
220B VAL* 3.8 2.9 - - - -
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 4.0 2.0 - - - -
174B VAL* 3.4 8.8 - - - +
175B SER* 2.8 38.7 + - - -
176B ALA* 3.1 23.9 + - - +
188B SER* 1.3 73.6 - - - +
190B SER* 1.3 63.6 + - - +
194B LEU 3.5 7.4 - - - -
195B CYS* 4.3 1.6 - - - -
217B VAL* 3.5 27.1 - - - -
219B PHE 3.8 0.7 - - - -
220B VAL* 3.4 16.3 + - - +
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 3.3 21.7 - - - +
172B ASP 3.1 13.0 + - - -
173B PRO 2.8 17.9 + - - -
175B SER* 4.0 1.3 - - - -
189B SER* 1.3 78.4 - - - +
191B TYR* 1.3 68.1 + - - +
192B ASP* 3.1 29.7 + - - +
193B GLY 3.1 11.3 + - - -
194B LEU 3.3 5.1 + - - -
217B VAL* 3.0 28.7 + - - +
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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
------------------------------------------------------------
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