Contacts of the strand formed by residues 180 - 186 (chain H) in PDB entry 2VT5
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 180 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175H LEU 3.6 2.8 - - - +
176H ALA* 3.5 1.1 - - - -
177H MET* 2.8 33.2 + - - +
178H ASP 3.0 3.6 + - - -
179H CYS* 1.3 83.6 - - - +
181H VAL* 1.3 64.1 + - - -
182H ASN* 4.2 5.4 - - - +
199H ASP* 4.2 8.7 - - - -
201H LYS* 5.0 1.6 - - - -
290H LYS* 4.3 16.4 - - - -
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Residues in contact with VAL 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H VAL* 3.5 30.3 - - + -
175H LEU 3.5 6.7 - - - +
176H ALA* 4.0 6.5 - - + -
180H GLY* 1.3 72.3 - - - -
182H ASN* 1.3 62.7 + - - +
199H ASP* 3.0 12.7 + - - +
200H VAL* 3.0 49.4 + - + +
256H LEU* 4.6 2.5 - - + -
287H VAL* 3.4 33.7 - - + +
290H LYS* 3.4 21.2 + - + -
291H ALA* 3.6 11.4 - - + +
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Residues in contact with ASN 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H PHE* 3.2 34.2 - - + -
174H VAL* 3.6 1.0 - - - -
175H LEU 2.9 34.9 + - - +
179H CYS* 4.0 14.4 - - - +
180H GLY 4.2 3.5 - - - +
181H VAL* 1.3 76.9 - - - +
183H CYS* 1.3 62.5 + - - +
184H PHE* 3.5 27.8 - - + -
195H LEU* 4.1 7.0 - - + +
197H ASP 3.6 1.8 - - - -
198H LYS* 3.4 15.2 - - - +
199H ASP* 3.0 27.1 - - - +
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Residues in contact with CYS 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H MET* 3.8 16.8 - - - -
173H LEU 3.6 3.8 - - - +
174H VAL* 4.0 22.2 - - - -
182H ASN* 1.3 73.5 - - - +
184H PHE* 1.3 60.6 + - - +
195H LEU* 3.7 2.6 - - - +
196H VAL* 2.9 28.5 + - - +
197H ASP* 2.8 38.6 + - + +
200H VAL* 3.7 28.7 - - - -
253H HIS* 5.0 2.5 - - - -
256H LEU* 4.8 5.2 - - - -
257H VAL* 6.4 0.7 - - - -
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Residues in contact with PHE 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H THR 4.0 2.7 - - - -
13H LEU* 3.5 60.1 - - + -
16H PHE* 3.7 25.8 - + + -
172H MET* 3.3 6.7 - - - +
173H LEU* 2.7 48.2 + - + +
175H LEU* 4.3 7.4 - - + -
182H ASN* 3.5 37.2 - - + -
183H CYS* 1.3 72.2 - - - +
185H MET* 1.3 61.8 + - - +
193H PHE* 3.8 21.2 - - + -
194H ILE 3.1 4.9 - - - +
195H LEU* 3.6 35.2 - - + -
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Residues in contact with MET 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G LYS* 3.8 32.8 - - + -
53G ILE* 3.8 30.7 - - + +
129G LEU* 4.1 14.4 - - + -
170H ALA* 3.8 19.3 - - - -
171H THR 3.6 16.2 - - - +
172H MET* 3.6 26.5 - - + -
184H PHE* 1.3 72.1 - - - +
186H LEU* 1.3 64.7 + - - +
187H ASP 3.3 3.1 + - - -
192H GLU 3.3 0.2 - - - +
193H PHE* 4.1 0.7 - - - -
194H ILE* 2.7 37.7 + - - +
196H VAL* 4.0 16.3 - - + +
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Residues in contact with LEU 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ARG 3.9 8.0 - - - +
50G LYS* 4.3 0.5 - - - +
42H LYS* 3.7 41.7 - - + +
45H SER* 3.7 29.2 - - - +
171H THR* 2.9 35.0 + - + +
184H PHE 3.8 2.2 + - - -
185H MET* 1.3 77.4 - - - +
187H ASP* 1.3 61.8 + - - +
188H PRO* 3.1 22.8 - - + +
191H GLY* 4.1 5.4 - - - -
192H GLU 3.5 20.6 - - - +
193H PHE* 3.5 22.2 - - + -
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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