Contacts of the strand formed by residues 150 - 155 (chain V) in PDB entry 1MVW
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 GLY 150 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142V LEU* 3.8 13.9 - - - +
149V THR* 1.3 78.5 - - - +
151V ILE* 1.3 63.0 + - - +
164V PRO* 3.7 0.5 - - - +
165V ILE* 2.9 28.9 + - - +
293V LEU* 3.8 11.7 - - - +
296V ASN* 3.2 20.6 - - - -
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Residues in contact with ILE 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142V LEU* 4.9 0.2 - - - -
150V GLY* 1.3 75.1 - - - +
152V VAL* 1.3 65.1 + - - +
153V LEU 4.0 0.3 + - - -
162V ASN* 4.5 6.7 - - + +
163V VAL 3.6 8.3 - - - +
164V PRO* 3.9 22.2 - - + -
278V THR* 3.6 29.6 - - + +
281V SER* 3.6 21.8 - - - +
282V ILE* 3.7 12.6 - - + +
293V LEU* 3.4 33.4 - - + +
296V ASN 2.8 8.4 + - - +
297V ASN* 3.4 21.7 - - - +
298V VAL 2.9 23.4 + - - +
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Residues in contact with VAL 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138V ALA* 3.3 41.1 - - + +
141V SER* 4.3 2.2 - - - -
142V LEU* 3.8 29.8 - - + +
151V ILE* 1.3 74.1 - - - +
153V LEU* 1.3 66.9 + - - +
154V ASP* 3.6 11.0 + - + +
162V ASN* 3.2 6.1 - - - -
163V VAL* 2.9 32.9 + - - +
165V ILE* 4.5 1.6 - - + -
298V VAL* 3.1 14.6 - - + +
300V SER* 3.6 24.5 - - - +
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Residues in contact with LEU 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151V ILE 4.0 0.8 + - - -
152V VAL* 1.3 71.5 - - - +
154V ASP* 1.3 58.9 + - - +
155V SER* 5.1 2.0 - - - -
160V THR* 4.4 8.7 - - + -
161V HIS 3.4 8.3 - - - +
162V ASN* 3.6 24.7 - - - +
274V ILE* 3.6 41.5 - - + +
277V THR* 5.9 0.2 - - + -
278V THR* 3.9 10.1 - - - +
297V ASN* 4.5 13.1 - - - +
298V VAL 2.9 8.4 + - - +
299V MET* 3.6 33.8 - - + +
300V SER 3.1 24.4 + - - +
304V THR* 4.0 14.1 - - + -
309V ILE* 5.7 4.5 - - + -
313V MET* 4.5 4.0 - - + -
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Residues in contact with ASP 154 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109V PRO* 5.9 1.9 - - - +
137V GLN* 4.0 26.5 - - - +
138V ALA* 4.1 10.7 + - + -
152V VAL* 3.6 12.9 + - + +
153V LEU* 1.3 72.7 - - - +
155V SER* 1.4 64.8 + - - +
159V VAL 4.0 1.3 - - - +
160V THR* 3.2 4.0 - - - +
161V HIS* 2.7 50.3 + - + +
300V SER* 3.0 30.2 + - - +
301V GLY* 4.0 4.2 + - - -
339V VAL* 4.2 9.3 - - - +
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Residues in contact with SER 155 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153V LEU* 5.1 3.8 - - - -
154V ASP* 1.4 75.5 + - - +
156V GLY* 1.3 61.4 + - - +
159V VAL 3.6 4.5 - - - -
160V THR* 2.6 27.4 + - - +
180V LEU 4.6 0.7 + - - -
181V ALA* 4.5 2.3 - - - +
261V LEU* 4.8 4.5 - - - +
274V ILE* 5.5 1.0 - - - +
300V SER 3.1 8.5 + - - -
301V GLY* 3.2 13.2 - - - -
303V THR* 3.1 39.0 + - - +
304V THR* 3.6 19.3 - - - -
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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