Contacts of the strand formed by residues 180 - 184 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ALA 3.1 13.8 + - - -
148F ALA* 3.0 17.5 - - + -
149F ILE 2.7 31.1 + - - -
174F ALA* 4.8 0.5 - - - +
179F ARG* 1.3 76.0 - - - +
181F VAL* 1.3 57.0 + - - +
182F ILE* 4.6 6.3 - - + -
255F ARG 5.3 1.1 - - - -
256F LYS* 3.5 50.0 - - + +
258F LEU* 4.0 13.2 - - + -
276F GLU* 3.3 47.3 - - + -
277F MET* 3.5 29.2 - - + -
280F ALA* 4.0 17.3 - - + -
281F TYR* 4.7 8.5 - + - -
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Residues in contact with VAL 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F ILE* 3.4 9.6 - - + +
151F VAL* 5.8 0.9 - - + -
171F LEU* 4.0 18.2 - - + -
174F ALA* 3.9 23.8 - - + -
175F ILE* 4.8 13.2 - - + -
179F ARG 3.6 5.5 + - - +
180F PHE* 1.3 77.2 - - - +
182F ILE* 1.3 64.5 + - - +
183F SER* 5.4 0.2 - - - -
191F PHE* 3.9 23.3 - - + -
201F LEU* 5.9 4.0 - - + -
256F LYS 3.1 8.0 + - - +
257F LEU* 3.4 27.8 - - + +
258F LEU 3.0 24.6 + - - -
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Residues in contact with ILE 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ILE* 5.1 0.7 - - + -
81F PRO* 5.7 2.5 - - + -
85F LEU* 4.5 13.2 - - + -
148F ALA* 3.8 26.2 - - + -
149F ILE 2.7 12.7 + - - +
150F PHE* 3.2 25.2 - - + -
151F VAL* 2.8 31.4 + - - +
180F PHE* 4.6 3.4 - - + -
181F VAL* 1.3 78.6 - - - +
183F SER* 1.3 62.0 + - - +
258F LEU* 3.3 17.9 - - + +
269F LEU* 3.8 30.5 - - + -
273F ALA* 4.0 25.1 - - + -
277F MET* 4.2 9.9 - - - -
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F PHE* 4.3 2.5 - - - -
151F VAL* 2.7 26.6 + - - +
182F ILE* 1.3 79.1 - - - +
184F LEU* 1.3 73.5 + - - +
187F GLY 3.1 3.6 - - - -
188F PRO* 3.1 23.0 - - - -
191F PHE* 4.1 24.0 - - - -
258F LEU 3.1 5.9 + - - +
259F THR* 3.1 28.4 - - - -
260F GLY 3.2 0.2 + - - -
269F LEU* 3.5 4.1 - - - +
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Residues in contact with LEU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F GLU* 3.6 29.2 - - + +
150F PHE* 4.0 20.2 - - + -
151F VAL 3.7 0.4 + - - -
152F PRO* 4.0 1.3 - - + -
153F GLY* 3.2 25.2 - - - +
183F SER* 1.3 84.8 + - - +
185F CYS* 1.3 69.4 - - - +
187F GLY 2.9 16.1 + - - -
188F PRO* 3.7 7.2 - - - -
260F GLY 3.4 23.1 - - - +
262F SER 3.8 20.6 - - - +
265F ALA* 4.5 3.8 - - + -
266F ALA* 4.2 17.3 - - - +
269F LEU* 3.8 14.8 - - + -
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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