Contacts of the strand formed by residues 150 - 155 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142W LEU* 3.8 14.1 - - - +
149W THR* 1.3 77.1 - - - +
151W ILE* 1.3 61.9 + - - +
164W PRO* 3.7 0.5 - - - +
165W ILE* 2.9 28.7 + - - +
292W ASP 4.8 0.2 - - - -
293W LEU* 3.8 12.5 - - - +
296W ASN* 3.2 20.9 - - - -
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Residues in contact with ILE 151 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150W GLY* 1.3 75.1 - - - +
152W VAL* 1.3 66.2 + - - +
153W LEU 4.0 0.2 + - - -
162W ASN* 4.5 5.8 - - + +
163W VAL 3.6 8.3 - - - +
164W PRO* 3.9 23.3 - - + -
278W THR* 3.6 29.4 - - + +
281W SER* 3.6 21.8 - - - +
282W ILE* 3.7 13.0 - - + -
293W LEU* 3.4 33.2 - - + +
296W ASN 2.8 8.6 + - - +
297W ASN* 3.4 21.1 - - - +
298W VAL 2.9 23.4 + - - +
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Residues in contact with VAL 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138W ALA* 3.3 42.0 - - + +
141W SER* 4.3 2.7 - - - -
142W LEU* 3.8 29.8 - - + +
151W ILE* 1.3 74.5 - - - +
153W LEU* 1.3 66.7 + - - +
154W ASP* 3.6 10.0 + - + +
161W HIS 3.6 0.3 - - - +
162W ASN* 3.2 6.5 - - - +
163W VAL* 2.9 32.1 + - - +
165W ILE* 4.5 1.6 - - + -
297W ASN* 5.6 0.2 - - - -
298W VAL* 3.1 14.6 - - + +
300W SER* 3.6 24.2 - - - +
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Residues in contact with LEU 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W ILE 4.0 1.0 + - - -
152W VAL* 1.3 71.9 - - - +
154W ASP* 1.3 59.1 + - - +
155W SER* 5.0 2.0 - - - -
160W THR* 4.4 8.3 - - + -
161W HIS 3.4 8.7 - - - +
162W ASN* 3.6 24.0 - - - +
274W ILE* 3.6 41.3 - - + +
278W THR* 3.9 10.3 - - - +
297W ASN* 4.5 13.7 - - - +
298W VAL 2.9 7.8 + - - +
299W MET* 3.6 35.2 - - + -
300W SER 3.1 24.4 + - - +
304W THR* 4.0 14.4 - - + -
309W ILE* 5.7 4.9 - - + -
313W MET* 4.5 3.4 - - + -
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Residues in contact with ASP 154 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109W PRO* 5.9 2.8 - - + +
137W GLN* 4.0 26.0 - - - +
138W ALA* 4.1 10.7 + - + +
152W VAL* 3.6 12.5 + - + +
153W LEU* 1.3 74.1 - - - +
155W SER* 1.4 64.1 + - - +
156W GLY 5.1 0.2 + - - -
159W VAL 4.0 1.1 - - - +
160W THR* 3.2 3.7 - - - +
161W HIS* 2.7 50.6 + - + +
300W SER* 3.0 30.6 + - - +
301W GLY* 4.0 4.3 + - - -
339W VAL* 4.2 9.9 - - - +
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Residues in contact with SER 155 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153W LEU* 5.0 3.8 - - - -
154W ASP* 1.4 76.1 + - - +
156W GLY* 1.3 62.4 + - - +
159W VAL 3.6 4.3 - - - -
160W THR* 2.6 27.6 + - - +
180W LEU 4.6 0.3 + - - -
181W ALA* 4.5 1.9 - - - +
261W LEU* 4.8 4.8 - - - +
274W ILE* 5.5 1.0 - - - +
300W SER 3.1 8.3 + - - -
301W GLY* 3.2 13.8 - - - -
303W THR* 3.1 38.7 + - - +
304W THR* 3.6 19.7 - - - -
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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