Contacts of the strand formed by residues 167 - 171 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ILE 3.0 6.3 + - - +
113F VAL* 3.4 5.9 - - + +
114F PHE* 3.0 26.0 + - - +
143F LYS* 3.2 23.8 - - + +
145F VAL* 4.3 13.5 - - + -
160F ALA* 3.8 42.2 - - + +
163F ASP* 4.0 18.2 - - + +
165F ASN 3.6 11.7 - - - +
166F PRO* 1.3 74.9 - - - +
168F VAL* 1.3 74.6 + - - +
169F VAL* 4.3 2.9 - - + -
195F ILE* 4.4 4.7 - - + -
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Residues in contact with VAL 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PHE* 3.4 34.3 - - + -
93F VAL* 4.6 3.6 - - + -
114F PHE* 3.2 20.9 - - + -
136F TYR* 4.4 15.9 - - + -
142F LEU* 4.2 30.5 - - + -
143F LYS 2.9 6.1 + - - -
144F VAL* 3.5 12.2 - - + -
145F VAL* 3.1 28.4 + - - +
167F VAL* 1.3 75.9 - - - +
169F VAL* 1.3 59.5 + - - +
170F LEU* 3.7 16.8 - - + -
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Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PHE* 3.7 2.6 - - - -
113F VAL* 4.0 8.3 - - + -
114F PHE 2.8 8.3 + - - -
115F ARG* 3.5 20.9 - - + -
116F GLY 3.5 9.4 + - - +
145F VAL* 3.6 23.1 - - + -
147F PRO* 4.2 14.6 - - + -
153F ALA 6.0 0.7 - - - +
156F LEU* 4.8 2.5 - - + +
157F ILE* 3.9 32.5 - - + +
160F ALA* 3.9 19.3 - - + -
167F VAL* 4.3 1.1 - - + -
168F VAL* 1.3 75.5 - - - +
170F LEU* 1.3 60.3 + - - +
171F GLU* 3.2 23.4 + - + +
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Residues in contact with LEU 170 (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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83F PHE* 3.6 38.1 - - + -
116F GLY 4.2 0.2 - - - -
118F ASN* 3.9 21.7 - - + +
132F PHE* 4.1 2.0 - - + +
133F ALA* 3.4 42.4 - - + +
136F TYR* 4.8 3.8 - - + -
144F VAL* 3.8 17.5 - - + -
145F VAL 2.8 17.4 + - - +
146F SER* 3.5 17.6 + - - +
147F PRO* 3.2 19.0 - - - +
168F VAL* 3.7 15.0 - - + -
169F VAL* 1.3 70.0 - - - +
171F GLU* 1.3 64.8 + - - +
172F ASN 3.9 0.3 + - - -
213F SER* 4.6 2.3 + - - -
241F ILE* 5.3 0.2 - - + -
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Residues in contact with GLU 171 (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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9F ILE* 3.6 26.5 - - + +
115F ARG* 2.4 48.0 + - - +
116F GLY 3.0 21.7 + - - +
117F PRO* 3.7 0.2 - - - -
118F ASN* 2.6 33.7 + - - +
147F PRO* 4.4 10.8 - - + -
157F ILE* 4.6 1.2 - - - +
169F VAL* 4.0 18.0 - - + +
170F LEU* 1.3 76.2 - - - +
172F ASN* 1.3 56.7 + - - +
176F TYR* 2.4 43.0 + - + +
213F SER* 5.1 0.2 + - - -
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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