Contacts of the strand formed by residues 172 - 176 (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 ILE 172 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G ALA* 3.7 32.1 - - + +
65G LEU* 3.7 35.7 - - + -
66G LEU* 3.8 23.6 - - + -
149G VAL 3.4 3.9 + - - +
150G VAL* 3.3 14.6 - - + +
151G GLU* 2.7 33.5 + - - +
170G GLY 3.3 0.8 - - - -
171G HIS* 1.3 88.1 - - + +
173G GLY* 1.3 64.2 + - - +
174G CYS* 4.3 1.1 - - - -
192G THR* 4.3 12.8 - - + -
193G LEU 3.4 7.2 - - - +
194G ILE* 4.7 3.8 - - + -
195G ASN* 4.4 3.4 - - - -
199G LEU* 4.3 8.7 - - + -
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Residues in contact with GLY 173 (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 GLU* 3.7 4.9 - - - -
167G GLY* 3.3 29.3 + - - -
172G ILE* 1.3 76.1 - - - +
174G CYS* 1.3 64.9 + - - -
192G THR* 3.5 4.2 - - - -
193G LEU* 2.6 47.5 + - - -
195G ASN* 4.1 0.6 - - - +
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Residues in contact with CYS 174 (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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55G CYS* 4.1 13.0 - - - -
58G SER* 3.6 31.2 - - - -
59G LEU* 3.6 29.2 - - + -
62G ALA* 4.5 0.2 - - - -
150G VAL* 4.2 12.3 - - - -
151G GLU* 2.8 17.8 + - - +
152G ASP* 4.5 1.6 - - - -
153G ALA* 3.0 31.4 + - - +
154G ALA* 3.4 1.2 + - - -
167G GLY* 4.8 1.0 - - - -
172G ILE* 4.3 4.9 - - - -
173G GLY* 1.3 79.5 - - - -
175G PHE* 1.3 63.9 + - - +
191G ALA 3.5 3.6 - - - -
192G THR* 5.3 0.2 - - - -
193G LEU* 4.1 0.6 - - - +
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Residues in contact with PHE 175 (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* 4.6 9.2 - - + -
44G PHE* 3.7 35.4 - + - -
55G CYS* 3.3 18.9 - - - +
153G ALA* 3.2 28.7 - - + -
154G ALA* 4.3 0.2 - - - -
157G VAL* 4.0 25.6 - - + -
158G MSE 5.1 0.2 - - - -
166G LEU 3.1 28.3 - - - -
167G GLY* 4.0 4.5 - - - -
174G CYS* 1.3 76.8 - - - +
176G SER* 1.3 59.6 + - - +
177G PHE* 4.2 16.4 - + + -
191G ALA* 3.0 44.2 + - + +
193G LEU* 3.6 25.5 - - + +
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Residues in contact with SER 176 (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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55G CYS* 3.5 14.6 - - - -
154G ALA* 3.3 38.0 + - - +
157G VAL* 5.1 6.7 - - - +
175G PHE* 1.3 75.6 - - - +
177G PHE* 1.3 73.3 + - - +
178G HIS 3.8 1.9 + - - -
181G LLP 2.7 53.6 + - - +
183G TYR 4.1 0.2 - - - +
189G GLY 4.1 0.7 - - - -
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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