Contacts of the strand formed by residues 163 - 169 (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 MET 163 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150R GLU* 3.2 3.7 - - - +
151R VAL* 2.9 9.0 - - - +
152R GLN* 2.8 45.4 + - - +
161R VAL* 3.1 40.4 - - + -
162R PRO* 1.3 73.7 + - - -
164R ALA* 1.3 60.6 + - - +
165R ARG* 3.8 23.3 - - + -
206R TRP* 3.5 38.1 - - + -
207R ILE 3.4 10.1 - - - +
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Residues in contact with ALA 164 (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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149R ALA* 6.5 0.2 - - + -
150R GLU 3.6 3.8 - - - -
151R VAL* 3.8 14.8 - - + +
162R PRO* 4.1 2.8 - - + +
163R MET* 1.3 71.4 - - - +
165R ARG* 1.3 58.9 + - - +
179R TRP* 3.8 24.1 + - + -
206R TRP* 3.4 0.9 - - - -
207R ILE* 2.7 56.3 + - + +
209R VAL* 5.3 2.5 - - + -
219R VAL* 4.9 6.5 - - + -
236R VAL* 4.6 8.5 - - + -
237R SER 4.9 1.1 - - - +
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Residues in contact with ARG 165 (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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148R THR 3.8 0.2 - - - +
149R ALA* 3.3 8.8 - - - +
150R GLU* 2.7 78.4 + - + +
163R MET* 3.7 22.4 + - + -
164R ALA* 1.3 74.7 - - - +
166R CYS* 1.3 62.3 + - - +
167R VAL* 3.7 29.1 + - - +
179R TRP* 3.9 2.5 - - - -
192R VAL* 6.0 2.2 - - - +
204R SER* 4.4 20.3 + - - -
205R LEU 3.7 4.7 - - - +
206R TRP* 3.6 17.9 - - + -
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Residues in contact with CYS 166 (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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147R ASN* 4.2 2.7 - - - -
148R THR 3.9 2.7 - - - -
165R ARG* 1.3 70.9 - - - +
167R VAL* 1.3 63.9 + - - +
168R SER 3.7 1.2 + - - -
177R ILE* 4.5 5.6 - - - +
179R TRP* 3.4 15.1 - - + +
204R SER* 3.7 0.7 - - - -
205R LEU* 2.6 38.2 + - + +
221R CYS* 2.0 49.4 - - - -
223R VAL* 3.7 16.8 - - - -
234R LEU* 3.7 14.1 - - + -
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Residues in contact with VAL 167 (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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147R ASN* 2.8 25.9 + - - -
148R THR* 3.2 34.8 + - - +
150R GLU* 5.3 7.0 - - + +
165R ARG* 3.7 28.3 - - - +
166R CYS* 1.3 71.5 - - - +
168R SER* 1.3 66.2 + - - +
169R THR* 4.1 13.9 - - + +
202R VAL* 5.5 3.1 - - + -
203R THR 4.3 1.1 - - - +
204R SER* 3.4 22.2 - - - +
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Residues in contact with SER 168 (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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145R PRO* 4.2 6.6 - - - +
146R GLN 3.5 1.1 - - - -
147R ASN* 3.2 25.4 + - - +
166R CYS 3.7 0.6 + - - -
167R VAL* 1.3 72.1 - - - +
169R THR* 1.3 58.9 + - - +
170R GLY 3.9 0.2 + - - -
175R ALA* 3.9 21.0 - - - +
177R ILE* 4.0 10.5 - - - -
201R THR 4.7 0.5 - - - +
202R VAL* 3.3 5.2 - - - +
203R THR* 2.7 55.5 + - - +
223R VAL* 4.1 0.2 - - - +
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Residues in contact with THR 169 (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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145R PRO* 4.7 0.7 - - - -
146R GLN* 2.9 54.1 + - + +
147R ASN* 5.6 1.1 - - - -
167R VAL* 5.0 13.2 - - + -
168R SER* 1.3 73.1 - - - +
170R GLY* 1.3 63.1 + - - +
202R VAL* 3.7 13.8 - - - +
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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