Contacts of the strand formed by residues 180 - 184 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ALA* 3.2 21.3 + - + +
148G ALA* 3.2 11.7 - - + -
149G ILE* 2.8 26.1 + - - +
174G ALA* 4.9 0.2 - - - +
179G ARG* 1.3 77.5 - - - +
181G VAL* 1.3 62.4 + - - +
182G ILE* 4.4 4.0 - - + -
255G ARG 4.8 1.8 - - - -
256G LYS* 3.5 53.2 - - + -
258G LEU* 4.0 14.1 - - + -
276G GLU* 3.4 44.4 - - + -
277G MET* 3.4 32.5 - - + -
280G ALA* 4.6 9.2 - - + -
281G TYR 6.1 2.5 - - - -
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Residues in contact with VAL 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G ILE* 3.5 9.4 - - + +
151G VAL* 5.8 1.8 - - + -
171G LEU* 4.2 15.0 - - + -
174G ALA* 4.1 22.4 - - + -
175G ILE* 4.8 12.6 - - + -
179G ARG 3.8 6.5 + - - +
180G PHE* 1.3 79.6 - - - +
182G ILE* 1.3 66.4 + - - +
191G PHE* 3.9 22.2 - - + -
201G LEU* 5.9 2.9 - - + -
256G LYS 3.1 8.4 + - - +
257G LEU* 3.5 26.4 - - + +
258G LEU 3.0 26.5 + - - +
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Residues in contact with ILE 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 5.5 0.9 - - + -
81G PRO* 5.5 2.0 - - + -
85G LEU* 4.8 8.3 - - + -
148G ALA* 3.6 31.0 - - + -
149G ILE 2.9 9.0 + - - +
150G PHE* 3.2 32.1 - - + -
151G VAL* 2.7 33.1 + - - +
180G PHE* 4.4 3.6 - - + -
181G VAL* 1.3 81.2 - - - +
183G SER* 1.3 59.8 + - - +
258G LEU* 3.4 15.9 - - + +
269G LEU* 3.8 26.7 - - + -
273G ALA* 4.4 18.4 - - + -
277G MET* 4.1 15.3 - - + -
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Residues in contact with SER 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G VAL* 2.6 27.4 + - - +
181G VAL* 4.3 0.4 - - - -
182G ILE* 1.3 78.4 - - - +
184G LEU* 1.3 72.8 + - - +
187G GLY 3.1 20.1 - - - -
188G PRO* 3.9 10.8 - - - -
191G PHE* 4.1 21.7 - - - -
257G LEU* 5.9 0.2 - - - +
258G LEU 3.2 6.1 + - - -
259G THR* 3.2 26.6 - - - -
260G GLY 3.3 0.3 + - - -
269G LEU* 3.4 3.7 - - - +
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Residues in contact with LEU 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G GLU* 3.7 39.3 - - + +
81G PRO* 5.4 0.2 - - + -
150G PHE* 4.0 11.9 - - + -
151G VAL 3.7 0.4 + - - -
152G PRO* 4.1 0.7 - - + -
153G GLY* 3.3 22.2 + - - +
183G SER* 1.3 84.3 + - - +
185G CYS* 1.3 66.7 + - - +
187G GLY 3.0 14.7 + - - -
188G PRO* 3.7 6.0 - - - +
260G GLY 3.1 22.7 - - - +
262G SER 3.6 22.2 - - - +
265G ALA* 4.5 3.4 - - + -
266G ALA* 4.2 17.0 - - - +
269G LEU* 3.8 18.6 - - + -
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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