Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 4ZPK
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.0 8.7 - - - +
172A ALA* 2.9 9.7 + - - -
173A ASP* 1.3 73.5 - - - +
175A PHE* 1.3 65.3 + - - +
192A SER* 3.3 16.1 - - - -
196A VAL* 3.3 15.8 - - - +
340A ILE* 5.0 2.7 - - - -
341A GLY 3.0 14.6 - - - -
342A ARG* 4.0 3.4 - - - -
91B TYR* 4.8 1.1 + - - -
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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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174A GLY* 1.3 76.8 - - - +
176A LEU* 1.3 71.1 + - - +
177A PHE* 3.5 27.1 - + + -
189A VAL* 3.6 22.7 - - + -
190A SER* 4.5 2.2 - - - -
192A SER* 3.6 6.1 - - - -
193A VAL* 3.6 35.4 - - + +
196A VAL* 4.1 10.8 - - + -
197A LEU* 3.9 23.6 - - + -
204A TRP* 3.9 25.6 - + - -
267A MET* 4.6 7.4 - - - -
306A VAL* 5.4 1.8 - - + -
340A ILE* 3.3 8.9 - - - +
341A GLY* 2.9 40.8 + - - -
91B TYR* 3.6 10.1 - - - -
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Residues in contact with LEU 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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175A PHE* 1.3 78.4 - - - +
177A PHE* 1.3 67.5 + - - +
178A ILE* 4.0 5.8 - - + -
188A TYR* 3.5 26.2 - - + -
189A VAL* 3.3 2.3 - - - -
190A SER* 2.8 27.0 + - - -
338A VAL* 3.6 28.3 - - + -
339A ALA 3.1 25.1 - - - +
340A ILE* 4.2 6.7 - - + -
87B MET* 3.3 31.6 - - + +
90B LEU* 5.1 3.4 - - + +
91B TYR* 3.0 39.6 + - + +
94B ALA* 4.7 2.7 - - + -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 3.5 30.5 - + + -
176A LEU* 1.3 77.1 - - - +
178A ILE* 1.3 67.3 + - - +
179A VAL* 4.3 16.4 - - + -
186A VAL* 5.6 1.6 - - + -
188A TYR 3.2 13.9 - - - +
189A VAL* 4.3 4.5 - - + -
204A TRP* 4.8 8.3 - + - +
209A LEU* 4.7 20.6 - - + -
263A PHE* 6.4 1.3 - + - -
267A MET* 4.6 9.6 - - + -
308A CYS* 3.9 22.7 - - + -
337A LEU* 4.1 6.9 - - + +
338A VAL* 3.8 0.2 - - - -
339A ALA* 2.9 55.0 + - + +
340A ILE 4.1 1.6 - - - -
341A GLY* 3.5 27.1 - - - -
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Residues in contact with ILE 178 (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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176A LEU* 4.0 11.0 - - + -
177A PHE* 1.3 78.3 - - - +
179A VAL* 1.3 59.0 + - - +
187A VAL* 2.6 43.4 + - + -
188A TYR* 2.9 54.7 + - + +
336A CYS* 4.1 16.2 - - + -
337A LEU 3.2 15.0 - - - +
338A VAL* 3.5 31.2 - - + -
87B MET* 3.7 18.4 - - + -
90B LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 179 (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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177A PHE* 4.3 18.8 - - + -
178A ILE* 1.3 80.1 - - - +
180A SER* 1.3 77.9 + - - +
181A CYS 3.3 0.2 + - - -
184A GLY* 3.2 27.4 - - - +
185A ARG 3.3 6.3 - - - +
186A VAL* 3.8 19.3 - - + -
187A VAL* 4.0 1.1 - - - -
209A LEU* 4.2 26.5 - - + -
225A LEU* 5.7 7.1 - - + +
336A CYS* 4.0 4.3 - - - -
337A LEU* 2.9 38.8 + - + +
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Residues in contact with SER 180 (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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179A VAL* 1.3 82.6 - - - +
181A CYS* 1.3 66.5 + - - +
182A GLU 3.1 3.5 + - - -
183A THR* 2.2 31.0 + - - -
184A GLY* 3.5 6.4 + - - -
185A ARG* 3.3 39.3 + - - +
187A VAL* 3.7 4.9 - - - +
225A LEU* 5.3 0.9 - - - +
335A PHE 4.7 2.2 - - - -
336A CYS* 3.8 19.3 - - - -
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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