Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 4ZTZ
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 3.7 3.5 - - - +
173A GLU* 1.3 79.2 - - - +
175A TRP* 1.3 63.2 + - - -
187A VAL 4.6 1.6 - - - -
188A ALA* 5.7 1.6 - - - -
222A SER 3.5 1.4 - - - +
223A TRP* 3.2 20.0 - - - -
224A CYS 2.9 33.5 + - - -
243A ASP* 5.9 0.2 - - - -
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Residues in contact with TRP 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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173A GLU 5.0 1.6 - - - +
174A GLY* 1.3 74.8 - - - -
176A THR* 1.3 65.0 + - - +
177A ARG 4.2 0.2 - - - -
186A PRO* 3.9 1.6 - - - +
187A VAL* 2.8 47.0 + - + +
188A ALA 3.0 24.5 - - - +
190A PRO* 3.5 21.7 - - + +
197A PHE* 3.6 31.6 - + - -
212A ALA* 4.6 0.2 - - + -
213A VAL 4.9 0.4 - - - -
214A ALA* 3.9 15.5 - - + -
221A TYR* 3.6 36.8 - - + -
222A SER 3.7 2.5 - - - -
223A TRP* 3.4 49.7 - + + -
242A ALA* 4.6 3.4 - - + -
243A ASP* 2.9 25.9 + - - +
244A LEU* 3.6 23.1 - - + -
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ALA* 3.7 22.9 - - + +
172A ALA* 4.4 23.8 - - + +
173A GLU 5.6 0.4 - - - +
174A GLY 5.1 0.2 - - - -
175A TRP* 1.3 80.5 - - - +
177A ARG* 1.3 60.4 + - - +
178A TYR* 2.9 19.5 + - - -
184A ALA* 5.3 1.6 - - + -
185A VAL 3.7 8.3 - - - -
186A PRO* 5.1 7.0 - - + -
221A TYR* 3.2 8.0 - - - -
222A SER* 2.3 60.2 + - - +
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Residues in contact with ARG 177 (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 TRP 4.2 0.6 - - - -
176A THR* 1.3 70.5 - - - +
178A TYR* 1.3 68.5 + - - +
179A GLY* 4.1 11.2 - - - +
180A PRO* 5.3 2.4 - - - +
183A GLU 2.8 14.7 - - - +
184A ALA* 3.9 0.5 - - - -
185A VAL* 2.9 43.3 + - + +
187A VAL* 3.8 12.4 - - + +
191A GLU 5.8 0.2 + - - -
192A GLU* 4.0 8.5 + - - -
218A SER* 4.6 7.7 - - - -
219A ALA* 3.5 27.2 - - - +
220A TRP 3.5 13.7 - - - -
221A TYR* 2.8 41.9 + - + -
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Residues in contact with TYR 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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163A PRO* 5.4 0.9 - - - +
166A PRO* 3.4 28.7 - - + -
168A ALA 3.9 16.4 - - - -
169A TRP* 3.6 14.8 - + - -
170A ALA* 2.8 28.8 + - + +
176A THR* 2.9 19.9 + - - -
177A ARG* 1.3 71.6 - - - +
179A GLY* 1.3 62.4 + - - +
182A GLY* 3.6 21.8 - - - -
183A GLU 3.3 11.4 - - - +
184A ALA* 4.5 12.6 - - + -
219A ALA* 3.1 4.0 - - - +
220A TRP* 2.9 52.3 + - + +
221A TYR 4.2 0.4 - - - -
222A SER* 2.6 38.2 + - - -
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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