Contacts of the strand formed by residues 180 - 184 (chain H) in PDB entry 1PV2
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 PHE 180 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ALA 3.0 16.6 + - - +
148H ALA* 3.1 13.0 - - + -
149H ILE* 2.9 26.0 + - - +
174H ALA* 4.5 0.7 - - - +
178H ASP 5.4 0.2 - - - -
179H ARG* 1.3 78.9 - - - +
181H VAL* 1.3 61.2 + - - +
182H ILE* 4.7 4.5 - - + -
255H ARG 4.7 4.3 - - - -
256H LYS* 3.4 56.5 - - + -
258H LEU* 4.2 15.9 - - + -
276H GLU* 3.4 41.3 - - + -
277H MET* 3.7 21.8 - - + -
280H ALA* 4.0 17.0 - - + -
281H TYR* 5.1 6.1 - + - -
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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
----------------------------------------------------------
149H ILE* 3.6 8.7 - - + +
151H VAL* 5.5 0.2 - - + -
171H LEU* 3.8 25.4 - - + -
174H ALA* 4.1 14.1 - - + -
175H ILE* 3.7 28.9 - - + -
179H ARG 4.2 5.2 - - - +
180H PHE* 1.3 77.7 - - - +
182H ILE* 1.3 66.8 + - - +
191H PHE* 4.1 13.7 - - + -
201H LEU* 5.1 3.4 - - + -
256H LYS* 2.9 11.0 + - + +
257H LEU* 3.3 28.2 - - + +
258H LEU 3.0 24.4 + - - -
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Residues in contact with ILE 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H PRO* 5.8 2.5 - - + -
85H LEU* 4.2 15.0 - - + -
148H ALA* 3.9 24.5 - - + -
149H ILE 2.9 10.8 + - - +
150H PHE* 3.8 27.1 - - + -
151H VAL* 2.9 27.2 + - - +
180H PHE* 4.7 1.6 - - + -
181H VAL* 1.3 83.6 - - - +
183H SER* 1.3 67.8 + - - +
191H PHE* 5.4 0.2 - - - -
258H LEU* 3.3 24.0 - - + +
259H THR* 5.1 0.2 - - - -
269H LEU* 3.9 25.1 - - + -
273H ALA* 4.2 22.2 - - + -
277H MET* 4.6 7.0 - - - -
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Residues in contact with SER 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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150H PHE* 4.5 0.2 - - - -
151H VAL* 2.5 29.7 + - - +
182H ILE* 1.3 77.9 - - - +
184H LEU* 1.3 70.0 + - - +
187H GLY 3.0 21.1 - - - -
188H PRO* 3.8 15.7 - - - +
191H PHE* 4.0 14.5 - - - -
258H LEU 3.1 6.7 + - - -
259H THR* 3.2 10.9 - - - +
260H GLY 3.1 14.8 + - - -
269H LEU* 3.2 8.0 - - - +
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Residues in contact with LEU 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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77H GLU* 3.7 48.2 - - + +
81H PRO* 4.9 0.2 - - + -
150H PHE* 4.1 8.1 - - + -
152H PRO* 3.8 7.6 - - + -
153H GLY* 3.2 25.4 - - - +
183H SER* 1.3 84.9 + - - +
185H CYS* 1.3 68.3 + - - +
187H GLY* 2.8 19.4 + - - -
188H PRO* 3.7 5.6 - - - +
260H GLY 3.0 24.5 - - - +
262H SER 4.0 13.0 - - - +
265H ALA 4.7 1.6 - - - -
266H ALA* 4.2 13.2 - - - +
269H LEU* 3.8 14.4 - - + -
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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