Contacts of the strand formed by residues 190 - 194 (chain G) in PDB entry 4PIW
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 190 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51G LEU* 3.3 8.0 - - - +
52G THR* 2.4 51.3 + - - +
54G SER 3.5 11.2 - - - -
175G PHE 3.6 7.0 - - - -
177G PHE* 3.5 12.9 - - - -
189G GLY* 1.3 74.3 - - - -
191G ALA* 1.3 56.3 + - - +
235G MSE 4.8 0.8 - - - +
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Residues in contact with ALA 191 (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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40G LEU* 4.5 0.7 - - + -
49G VAL* 4.2 13.0 - - + -
50G LEU 3.5 5.8 - - - +
51G LEU* 3.9 12.3 - - + -
58G SER* 2.9 16.7 + - - -
174G CYS* 3.5 1.6 - - - -
175G PHE* 3.0 45.0 + - + -
177G PHE* 3.6 19.9 - - + -
190G GLY* 1.3 75.1 - - - +
192G THR* 1.3 59.8 + - - +
193G LEU* 4.0 1.1 - - + -
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Residues in contact with THR 192 (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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48G LYS 3.6 1.4 - - - +
49G VAL* 3.4 2.4 - - - -
50G LEU* 2.7 42.8 + - - +
52G THR* 3.3 13.7 - - - +
58G SER* 3.0 31.3 + - - +
61G MSE 3.5 23.1 - - + -
62G ALA 5.4 0.9 - - - +
65G LEU* 5.4 1.1 - - + -
172G ILE* 4.3 11.9 - - + -
173G GLY 3.5 6.3 - - - +
191G ALA* 1.3 71.3 - - - +
193G LEU* 1.3 62.4 + - - +
194G ILE* 3.6 24.6 + - + +
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Residues in contact with LEU 193 (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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40G LEU* 5.5 0.7 - - + +
44G PHE* 5.1 6.1 - - + -
46G SER* 3.6 24.7 - - - +
48G LYS 3.4 4.5 - - - -
49G VAL* 3.7 15.0 - - + -
167G GLY 3.4 29.4 - - - +
168G THR* 4.4 4.5 - - - +
172G ILE* 3.4 6.6 - - - +
173G GLY* 2.6 53.5 + - - +
174G CYS 4.1 0.4 - - - +
175G PHE* 3.6 53.2 - - + +
191G ALA* 4.4 3.6 - - + +
192G THR* 1.3 71.2 - - - +
194G ILE* 1.3 62.7 + - - +
195G ASN* 3.6 2.2 + - - +
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Residues in contact with ILE 194 (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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47G ALA* 3.3 5.4 - - - +
48G LYS* 2.4 61.7 + - + +
50G LEU* 4.8 4.5 - - + -
61G MSE 5.0 0.4 - - + -
65G LEU* 3.7 24.2 - - + -
171G HIS 4.2 3.6 - - - +
172G ILE* 4.7 6.1 - - + -
192G THR* 3.7 30.7 - - + +
193G LEU* 1.3 67.8 - - - +
195G ASN* 1.3 62.2 + - - +
196G ASP 3.3 20.9 - - - +
199G LEU* 3.9 18.4 - - + -
200G ILE* 3.7 14.3 - - + +
203G ALA* 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