Contacts of the strand formed by residues 203 - 207 (chain R) in PDB entry 3EPD
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 THR 203 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168R SER* 2.7 59.8 + - - +
174R PRO* 5.5 7.4 - - + -
175R ALA 4.2 17.5 - - - +
177R ILE* 3.1 24.7 - - + +
191R GLN* 3.4 9.7 - - - +
192R VAL* 2.5 27.9 + - - -
193R PRO* 4.0 4.3 - - - -
194R GLY* 5.2 0.4 - - - -
201R THR* 5.8 1.3 - - + +
202R VAL* 1.3 77.7 - - - +
204R SER* 1.3 64.1 + - - +
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Residues in contact with SER 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R ARG* 4.4 21.0 - - - -
166R CYS 3.7 6.3 - - - -
167R VAL* 3.4 25.7 - - - +
177R ILE* 4.1 1.6 - - - -
191R GLN 3.7 0.5 - - - -
192R VAL* 2.8 52.3 + - - +
202R VAL* 5.3 1.7 - - - +
203R THR* 1.3 85.5 + - - +
205R LEU* 1.3 60.4 + - - +
206R TRP* 3.8 3.9 - - - -
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Residues in contact with LEU 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165R ARG* 4.0 0.2 - - - +
166R CYS* 2.6 42.3 + - + +
177R ILE* 3.3 46.6 - - + +
178R THR 3.9 0.7 - - - +
179R TRP* 2.9 37.5 + - + +
189R THR* 3.4 29.6 - - - +
190R SER 3.4 16.8 - - - +
191R GLN* 3.7 23.6 - - + +
204R SER* 1.3 71.8 - - - +
206R TRP* 1.3 56.9 - - - +
221R CYS* 5.1 0.7 - - - -
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Residues in contact with TRP 206 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161R VAL* 3.1 36.3 - - + -
163R MET* 3.5 31.0 - - + -
164R ALA 3.4 5.2 - - - +
165R ARG* 3.6 14.1 - - + -
179R TRP* 3.7 1.3 - - - +
189R THR* 4.4 0.2 - - - -
190R SER* 3.2 42.9 + - - +
191R GLN 5.0 0.8 - - - -
192R VAL* 4.4 15.2 - - + +
204R SER 3.8 15.7 - - - -
205R LEU* 1.3 75.8 - - - +
207R ILE* 1.3 70.6 - - - +
208R LEU* 3.7 24.6 - - + +
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Residues in contact with ILE 207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R PRO* 3.4 0.9 - - - +
163R MET* 3.4 9.1 - - - +
164R ALA* 2.7 53.3 + - + +
179R TRP* 3.6 44.9 - - + -
180R HIS 6.0 0.2 - - - -
181R SER* 5.9 0.7 - - - -
186R MET* 5.2 1.3 - - + +
188R GLN 2.9 26.5 - - - +
189R THR* 4.0 5.2 - - - -
206R TRP* 1.3 80.4 - - - +
208R LEU* 1.3 64.1 + - - +
209R VAL* 3.4 20.1 - - + +
219R VAL* 3.7 24.2 - - + -
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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