Contacts of the strand formed by residues 135 - 141 (chain A) in PDB entry 2VSH
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 ALA 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ALA* 5.8 1.3 - - - +
133A HIS* 3.4 5.5 - - - +
134A ASP* 1.3 78.6 - - - +
136A VAL* 1.3 70.6 + - - +
172A THR 3.1 13.9 - - - +
173A PHE* 3.9 12.6 - - + -
197A CYS* 5.0 2.7 - - - -
200A PHE* 3.9 22.9 - - + -
206A ASP 3.1 5.6 + - - +
207A VAL* 3.4 18.3 - - + -
208A ALA 3.0 21.7 + - - -
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Residues in contact with VAL 136 (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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126A ASN* 3.6 25.8 - - - +
129A LEU* 3.6 17.9 - - + -
130A ALA* 3.5 35.7 - - + +
135A ALA* 1.3 81.3 - - - +
137A ASP* 1.3 62.6 + - - +
138A THR 4.2 0.2 - - - -
170A PRO 4.1 0.2 - - - +
171A GLN* 3.2 6.8 - - - -
172A THR* 2.8 31.9 + - - +
197A CYS* 3.7 4.3 - - - -
207A VAL* 4.1 2.7 - - - -
208A ALA* 3.4 10.8 - - + +
210A ALA* 3.5 31.6 - - + +
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Residues in contact with ASP 137 (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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136A VAL* 1.3 76.1 - - - +
138A THR* 1.3 67.5 + - - +
139A VAL* 3.5 13.2 + - + +
167A GLY* 5.0 1.1 - - - -
168A GLN 3.6 9.5 + - - +
170A PRO 4.0 0.9 - - - -
171A GLN* 3.2 21.7 - - - +
195A ASP* 4.9 0.9 - - - +
197A CYS* 3.5 23.0 - - - +
207A VAL* 4.0 0.8 - - + +
208A ALA 3.0 6.8 + - - +
209A LEU* 3.6 5.8 - - + -
210A ALA 2.9 21.3 + - - -
145B THR* 5.9 0.3 - - - +
147B VAL* 3.5 24.0 - - - +
155B ILE* 3.5 23.7 - - + +
158B ILE* 4.1 2.3 - - - +
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Residues in contact with THR 138 (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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122A MET* 5.0 4.9 - - + -
126A ASN* 2.9 24.0 + - - +
137A ASP* 1.3 72.0 + - - +
139A VAL* 1.3 54.8 + - - +
168A GLN* 2.7 38.1 + - - +
169A THR 3.8 17.0 - - - +
170A PRO* 2.7 33.7 + - + -
210A ALA* 3.4 9.6 - - + +
211A LYS 3.8 5.4 - - - +
212A GLY* 3.3 32.5 - - - +
216A ASN* 4.9 1.1 - - - +
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Residues in contact with VAL 139 (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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137A ASP* 3.8 23.6 - - + +
138A THR* 1.3 81.2 - - - +
140A VAL* 1.3 62.4 - - - +
165A TYR* 3.7 29.6 - - + -
166A GLN 3.3 13.7 - - - +
167A GLY* 4.1 7.0 - - - -
168A GLN* 4.4 1.6 - - - +
209A LEU* 4.1 23.1 - - + -
210A ALA 2.9 16.5 + - - +
211A LYS* 3.7 3.3 - - - +
212A GLY* 2.7 27.5 + - - -
147B VAL* 4.2 17.9 - - + -
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Residues in contact with VAL 140 (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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139A VAL* 1.3 73.1 - - - +
141A GLU* 1.3 58.4 + - - +
165A TYR* 3.1 11.0 - - - -
166A GLN* 2.7 53.9 + - + +
168A GLN* 3.7 17.9 - - - +
211A LYS* 6.1 0.4 - - + -
212A GLY 3.5 8.7 - - - +
213A GLU* 3.4 41.3 - - - +
214A TYR* 3.6 31.0 - - + +
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Residues in contact with GLU 141 (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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140A VAL* 1.3 76.7 - - - +
142A ALA* 1.3 66.3 + - - +
143A VAL* 3.5 2.0 + - + -
164A LEU 4.2 2.7 - - - +
165A TYR* 4.0 22.1 - - + -
166A GLN* 4.8 0.5 + - - +
214A TYR* 2.6 38.5 + - - +
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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