Contacts of the strand formed by residues 167 - 171 (chain X) in PDB entry 3EXG
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 167 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X ILE* 3.2 5.3 + - - +
113X VAL* 3.4 7.8 - - + +
114X PHE* 2.8 27.3 + - - +
143X LYS* 3.5 23.8 - - + +
145X VAL* 4.8 7.6 - - + -
160X ALA* 3.6 31.0 - - + +
163X ASP* 4.0 24.2 - - + +
165X ASN 3.1 16.2 + - - +
166X PRO* 1.3 76.2 - - - +
168X VAL* 1.3 65.6 + - - +
169X VAL* 3.8 9.6 + - + -
195X ILE* 4.4 9.2 - - + -
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Residues in contact with VAL 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X PHE* 3.9 15.7 - - + -
93X VAL* 4.6 2.5 - - + -
114X PHE* 3.4 23.3 - - + -
136X TYR* 4.2 21.8 - - + -
142X LEU* 4.1 28.5 - - + -
143X LYS 2.9 10.6 + - - +
144X VAL* 3.6 5.6 - - + +
145X VAL 3.1 26.0 + - - +
166X PRO 5.4 0.2 - - - -
167X VAL* 1.3 75.6 - - - +
169X VAL* 1.3 59.4 + - - +
170X LEU* 3.6 29.6 + - + -
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Residues in contact with VAL 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X PHE* 3.5 5.8 - - - -
113X VAL* 4.0 11.9 - - + -
114X PHE 2.6 16.7 + - - +
115X ARG* 3.3 23.1 - - + -
116X GLY 3.5 0.9 + - - -
145X VAL* 3.7 18.8 - - + -
147X PRO* 4.1 17.0 - - + -
156X LEU* 5.7 0.7 - - + -
157X ILE* 4.1 17.9 - - + +
160X ALA* 3.9 27.8 - - + -
167X VAL* 4.1 3.8 - - + -
168X VAL* 1.3 71.9 - - - +
170X LEU* 1.3 60.2 + - - +
171X GLU* 3.3 22.3 + - + +
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Residues in contact with LEU 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X PHE* 3.7 27.8 - - + -
116X GLY 4.1 2.0 - - - -
118X ASN* 3.8 22.7 - - + +
132X PHE* 4.3 2.2 - - + +
133X ALA* 3.6 38.6 - - + +
136X TYR* 4.7 5.6 - - + -
144X VAL* 3.7 20.2 - - + -
145X VAL 2.9 13.9 + - - +
146X SER* 3.6 17.2 + - - +
147X PRO* 3.2 21.2 - - - +
168X VAL* 3.7 22.2 - - + -
169X VAL* 1.3 68.2 - - - +
171X GLU* 1.3 64.2 + - - +
212X HIS* 5.9 0.9 - - + -
213X SER* 4.9 2.1 + - - -
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Residues in contact with GLU 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ILE* 3.5 25.6 - - + +
115X ARG* 2.8 43.4 + - - +
116X GLY* 2.9 29.0 + - - +
117X PRO* 3.7 0.2 - - - -
118X ASN* 2.7 32.8 + - - +
147X PRO* 4.6 11.4 - - + -
157X ILE* 5.0 1.6 - - - +
169X VAL* 4.2 16.9 - - + +
170X LEU* 1.3 78.2 - - - +
172X ASN* 1.3 60.1 + - - +
176X TYR* 2.5 33.7 + - + +
213X SER* 4.8 2.0 + - - -
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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