Contacts of the strand formed by residues 164 - 170 (chain A) in PDB entry 4V0P
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 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.7 29.6 - - + -
124A TYR* 3.8 52.7 - - + +
158A LEU* 2.8 41.7 + - + +
159A GLN* 3.3 8.8 + - - +
162A PHE* 3.6 19.7 - - + +
163A GLY* 1.3 81.2 - - - +
165A GLU* 1.3 64.6 + - - +
166A LEU 4.0 0.5 + - - -
178A PHE* 3.9 19.7 - - + -
179A ALA 3.6 3.8 - - - +
180A THR* 5.6 0.7 - - - -
181A CYS* 3.7 3.5 - - - -
187A ASP* 6.3 0.2 - - + -
197A PRO* 4.3 6.1 - - + -
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Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 2.7 35.0 + - - -
164A ILE* 1.3 73.7 - - - +
166A LEU* 1.3 63.6 + - - +
167A MET* 3.6 31.7 + - + +
178A PHE* 3.3 8.3 - - - +
179A ALA* 2.6 39.0 + - - +
180A THR 4.5 1.1 - - - +
181A CYS* 3.5 35.5 - - - -
182A LEU 5.1 1.0 + - - +
289A HIS* 3.6 6.8 - - - -
292A LYS* 3.4 17.0 + - - -
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.1 20.2 - - + -
130A VAL* 4.6 0.2 - - + -
135A MET* 4.2 8.5 - - + -
151A PHE* 3.8 33.2 - - + -
155A SER* 4.5 19.9 + - - +
158A LEU* 4.6 12.6 - - + -
159A GLN* 5.5 1.4 - - - +
164A ILE 4.0 1.6 + - - -
165A GLU* 1.3 76.9 + - - +
167A MET* 1.3 60.5 + - - +
168A GLU 4.3 0.5 + - - -
176A TYR* 3.7 27.5 - - + -
177A ILE 3.6 11.2 - - - +
178A PHE* 3.5 32.1 - - + -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.6 34.1 - - + +
166A LEU* 1.3 78.4 - - - +
168A GLU* 1.3 65.0 + - - +
169A VAL* 3.4 3.6 + - + -
176A TYR* 3.3 3.5 - - - -
177A ILE* 2.8 55.9 + - + +
179A ALA* 4.1 22.9 - - + -
180A THR 5.7 0.9 - - - +
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 1.3 72.8 - - - +
169A VAL* 1.3 60.6 + - - +
170A ASP 3.6 17.0 - - - +
171A PRO* 3.6 19.3 - - + +
174A HIS* 2.9 38.5 + - - +
175A LEU 3.5 9.2 - - - +
176A TYR* 3.4 34.3 + - + -
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 3.4 3.3 + - + +
168A GLU* 1.3 75.8 - - - +
170A ASP* 1.3 63.3 + - + +
171A PRO* 4.0 7.1 - - - +
175A LEU* 2.9 33.1 + - + +
177A ILE* 3.6 50.0 - - + -
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLU* 3.6 3.7 - - - +
169A VAL* 1.3 82.9 - - + +
171A PRO* 1.3 62.4 - - - +
172A ILE* 3.2 19.1 + - - +
173A GLY* 3.1 24.1 + - - -
174A HIS* 2.8 32.2 + - - -
175A LEU* 3.1 24.6 + - + +
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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