Contacts of the strand formed by residues 194 - 197 (chain F) in PDB entry 4ILW
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 ILE 194 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F ILE* 4.2 6.9 - - + +
159F MET 3.0 6.5 + - - +
160F ILE* 3.4 16.1 - - + -
161F SER 2.9 25.5 + - - -
182F HIS 3.8 4.9 - - - +
183F ALA* 3.9 8.7 - - + -
192F GLY 4.4 0.7 - - - +
193F ASP* 1.3 73.2 - - - +
195F HIS* 1.3 70.6 + - - +
196F PHE* 3.8 32.5 - - + -
215F ALA* 4.4 2.5 - - + +
218F GLU* 3.8 16.4 - - + -
219F LEU* 3.6 46.7 - - + +
222F SER* 3.4 19.5 - - - +
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Residues in contact with HIS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F MET 4.9 1.3 + - - -
161F SER* 3.3 21.0 + - - +
163F ALA* 5.4 1.8 - - + -
167F HIS* 3.2 14.5 + + + +
169F ASP* 3.2 10.1 - - + -
173F PHE* 3.2 14.7 - - + -
181F ALA* 3.2 6.3 - - - +
182F HIS* 2.9 37.0 + + - +
184F TYR* 3.8 16.1 - + - -
190F LEU* 3.8 16.7 - - + +
193F ASP* 4.3 7.6 + - + +
194F ILE* 1.3 87.6 - - - +
196F PHE* 1.3 62.0 - - - +
302F ZN 2.1 40.1 - - - -
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Residues in contact with PHE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ILE* 4.7 4.5 - - + -
160F ILE* 3.4 27.8 - - + -
161F SER 2.8 16.4 + - - -
162F PHE* 3.4 37.4 - + + -
163F ALA 2.8 29.6 + - - +
173F PHE* 3.6 3.5 - - - -
180F LEU 3.8 2.2 - - - -
181F ALA* 3.7 14.8 - - + -
194F ILE* 3.8 19.5 - - + -
195F HIS* 1.3 75.0 - - - +
197F ASP* 1.3 58.8 + - - +
202F TRP* 3.6 19.7 - + + -
211F LEU* 3.8 14.8 - - + -
214F VAL* 3.8 18.4 - - + -
215F ALA* 3.7 30.3 - - + -
218F GLU* 4.8 0.4 - - + -
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Residues in contact with ASP 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F ALA 3.2 9.4 - - - +
164F VAL* 4.0 1.4 - - - -
173F PHE* 3.4 38.9 - - + +
174F ASP* 3.5 2.3 + - - +
175F GLY 3.2 5.9 + - - +
179F SER 3.5 2.1 - - - +
180F LEU 2.9 21.0 + - - +
196F PHE* 1.3 69.0 - - - +
198F ASP* 1.3 59.2 + - - +
199F ASP* 2.8 24.3 + - - +
200F GLU* 3.1 24.1 + - - +
202F TRP* 2.8 16.8 + - - -
303F CA 2.4 26.2 - - - -
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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
------------------------------------------------------------
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