Contacts of the strand formed by residues 172 - 176 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.8 30.3 - - + +
65A LEU* 3.8 27.1 - - + -
66A LEU* 3.7 34.3 - - + -
149A VAL 3.3 3.8 + - - +
150A VAL* 3.2 14.1 - - + -
151A GLU* 2.6 33.4 + - - +
167A GLY 4.6 0.2 - - - -
170A GLY 4.8 0.2 - - - -
171A HIS* 1.3 86.6 + - + +
173A GLY* 1.3 66.0 + - - +
192A THR* 3.9 15.0 - - + -
193A LEU 3.4 5.6 - - - +
194A ILE* 5.0 4.0 - - + -
195A ASN* 4.3 4.0 - - - -
199A LEU* 4.3 8.7 - - + -
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLU* 3.4 13.0 - - - -
167A GLY* 3.5 21.1 + - - -
172A ILE* 1.3 76.6 - - - +
174A CYS* 1.3 70.1 + - - -
192A THR* 3.5 3.3 - - - -
193A LEU* 2.9 37.1 + - - -
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Residues in contact with CYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A CYS* 3.7 19.3 - - - -
58A SER* 3.9 28.3 - - - -
59A LEU* 3.6 26.9 - - + -
62A ALA* 4.5 3.6 - - - -
150A VAL* 4.3 11.0 - - - -
151A GLU* 2.7 16.9 + - - +
152A ASP* 4.5 1.6 - - - -
153A ALA* 3.0 32.6 + - - +
154A ALA* 3.5 1.4 + - - -
172A ILE* 4.6 0.7 - - - -
173A GLY* 1.3 80.0 - - - -
175A PHE* 1.3 63.2 + - - +
191A ALA 3.4 4.5 - - - -
192A THR* 4.9 0.4 - - - -
193A LEU* 3.8 1.2 - - - +
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.5 8.1 - - + -
44A PHE* 3.7 32.8 - + - -
55A CYS* 3.3 12.0 - - - +
153A ALA* 3.2 26.9 - - + -
157A VAL* 4.0 24.5 - - + -
158A MSE 5.3 0.2 - - - -
166A LEU 3.1 28.9 - - - -
167A GLY* 4.3 0.2 - - - -
174A CYS* 1.3 77.2 - - - +
176A SER* 1.3 61.2 + - - +
177A PHE* 4.2 16.8 - + + -
190A GLY* 3.2 4.2 - - - -
191A ALA* 2.7 49.5 + - + -
193A LEU* 3.7 35.0 - - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A CYS* 3.5 12.1 - - - -
153A ALA 4.2 0.4 + - - -
154A ALA* 3.3 40.3 + - - +
157A VAL* 4.8 8.2 - - - +
175A PHE* 1.3 75.3 - - - +
177A PHE* 1.3 71.7 + - - +
178A HIS* 3.7 3.1 + - - +
181A LLP 3.1 51.3 + - - +
183A TYR 4.1 0.3 - - - +
189A GLY 4.0 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