Contacts of the strand formed by residues 179 - 183 (chain A) in PDB entry 2VZE
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 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A CYS* 3.6 57.2 - - + +
103A LEU* 4.4 6.5 - - + -
155A LYS 3.0 4.4 + - - -
156A ALA* 3.1 21.4 - - + -
157A ILE 2.9 25.2 + - - +
177A LEU* 3.6 5.9 - - - +
178A ARG* 1.3 104.0 - - - +
180A LYS* 1.3 67.0 + - - +
181A LEU* 4.0 18.2 - - + +
192A LEU* 4.1 15.0 - - + -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 3.5 12.8 - - + -
167A VAL* 4.7 1.3 - - + -
168A ASP* 2.6 29.9 + - - +
171A ALA* 4.1 15.1 - - + +
177A LEU* 4.1 22.2 - - + -
178A ARG 5.6 0.7 - - - -
179A ILE* 1.3 79.0 - - - +
181A LEU* 1.3 61.3 + - - +
190A GLY* 3.5 25.0 + - - +
191A TRP* 3.6 35.4 - - + +
192A LEU* 2.9 30.6 + - - +
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Residues in contact with LEU 181 (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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96A VAL* 4.1 15.0 - - + -
97A LEU* 3.8 29.4 - - + -
101A CYS* 3.9 21.8 - - - -
103A LEU* 5.5 1.3 - - + -
156A ALA* 5.9 0.2 - - + -
157A ILE 2.9 12.2 + - - +
158A VAL* 3.3 21.2 - - + +
159A ALA 3.0 25.8 + - - +
179A ILE* 4.0 16.6 - - + -
180A LYS* 1.3 71.9 - - - +
182A LEU* 1.3 59.0 + - - +
183A VAL 4.0 0.2 + - - -
191A TRP* 3.6 3.7 - - - -
192A LEU* 3.5 24.9 - - + +
194A PHE* 4.1 25.1 - - + -
197A LEU* 4.3 2.9 - - + -
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Residues in contact with LEU 182 (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 ALA* 3.4 15.9 - - + +
160A GLY* 3.7 23.6 - - - +
161A ASP* 4.2 7.4 - - - +
164A ILE* 4.4 15.0 - - + -
181A LEU* 1.3 71.7 - - - +
183A VAL* 1.3 62.4 + - - +
184A SER* 3.8 13.6 + - - -
186A LYS* 4.1 17.9 - - + +
188A CYS* 3.8 31.4 - - + +
191A TRP* 3.7 28.2 - - + -
192A LEU 2.8 11.7 + - - +
193A ASN* 3.9 4.9 - - - +
194A PHE* 3.0 24.9 + - - -
195A LYS 4.5 0.5 + - - -
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Residues in contact with VAL 183 (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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113A LEU* 3.7 29.2 - - + -
116A VAL* 4.8 4.9 - - + -
118A GLU* 3.4 42.0 - - + +
122A VAL* 5.2 0.2 - - + -
158A VAL* 4.0 18.6 - - + -
159A ALA 2.8 8.7 + - - -
160A GLY* 3.6 17.0 - - - -
161A ASP* 4.2 1.9 + - - -
182A LEU* 1.3 70.7 - - - +
184A SER* 1.3 65.0 + - - +
194A PHE* 4.0 20.9 - - + -
195A LYS* 4.0 13.2 - - + -
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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