Contacts of the strand formed by residues 163 - 168 (chain M) in PDB entry 2ZHX
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 LEU 163 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60M VAL* 4.5 2.9 - - + -
61M ARG* 3.3 27.6 - - - +
62M VAL 3.8 1.1 - - - +
63M LEU* 3.7 20.4 - - + +
153M ILE* 5.1 1.1 - - + +
156M LEU* 3.9 46.0 - - + +
157M ALA 4.3 1.6 - - - +
159M ARG* 4.1 8.5 - - - +
161M ALA 4.0 1.1 + - - +
162M PRO* 1.3 76.3 - - - +
164M VAL* 1.3 77.9 + - - +
165M ALA* 4.0 2.0 + - + +
179M LEU* 4.2 22.7 - - + -
183M ASN 3.3 6.4 + - - +
184M CYS* 3.4 15.7 - - - +
185M VAL 3.1 25.1 + - - +
217M MET* 4.5 1.3 - - - +
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Residues in contact with VAL 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M ARG 2.8 12.9 + - - +
62M VAL* 2.9 16.5 - - + +
63M LEU 2.8 22.6 + - - -
163M LEU* 1.3 76.4 - - - +
165M ALA* 1.3 62.4 + - - +
166M ILE* 4.5 8.1 - - + -
185M VAL 3.4 6.5 - - - +
187M ILE* 4.6 2.7 - - + -
210M ALA* 3.7 35.4 - - + +
213M LEU* 3.8 17.3 - - + -
214M LEU* 3.8 22.9 - - + -
217M MET* 3.7 25.8 - - + -
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Residues in contact with ALA 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M LEU* 3.3 23.1 - - + +
163M LEU* 4.0 2.2 - - + -
164M VAL* 1.3 75.1 - - - +
166M ILE* 1.3 62.6 + - - +
167M LEU* 3.4 16.5 - - + +
179M LEU* 3.9 28.0 - - + -
185M VAL 3.0 9.3 + - - +
186M ALA* 3.3 3.9 - - + -
187M ILE* 2.8 26.9 + - - +
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Residues in contact with ILE 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62M VAL* 4.2 19.1 - - + -
63M LEU 2.7 17.2 + - - +
64M ILE* 3.5 29.7 - - + +
65M VAL* 3.7 15.8 + - - +
164M VAL* 4.5 5.8 - - + -
165M ALA* 1.3 75.4 - - - +
167M LEU* 1.3 62.4 + - - +
168M TRP* 3.2 44.5 + - + +
187M ILE* 3.4 31.9 - - + -
206M PRO* 4.3 12.6 - - + -
207M PHE* 5.0 5.4 - - + -
210M ALA* 4.6 5.8 - - + -
224M TRP* 5.6 1.6 - - + -
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Residues in contact with LEU 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M VAL* 4.2 11.4 - - + -
165M ALA* 3.4 35.9 - - + +
166M ILE* 1.3 76.5 - - - +
168M TRP* 1.3 64.1 + - - +
169M GLY 3.8 3.8 + - - +
172M ALA* 3.0 41.5 - - + +
173M SER* 4.1 7.6 - - - +
175M LEU* 4.5 5.2 - - + -
176M LYS* 4.3 20.0 - - + +
179M LEU* 5.5 3.6 - - + -
186M ALA* 4.1 11.9 - - + -
187M ILE 2.8 13.1 + - - +
188M GLU* 3.6 15.2 - - + +
189M SER 3.5 22.5 + - - +
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Residues in contact with TRP 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M ILE* 3.6 27.8 - - + -
65M VAL 4.7 8.5 + - - +
67M GLN* 5.1 3.1 + - - -
81M PHE* 3.3 29.5 - + + -
97M ILE* 3.1 44.2 - - + -
118M TRP* 5.6 2.0 - + - -
166M ILE* 3.2 36.1 + - + +
167M LEU* 1.3 74.3 - - - +
169M GLY* 1.3 59.3 + - - +
172M ALA* 3.8 11.3 + - - +
187M ILE 5.7 0.7 - - - -
188M GLU 5.7 0.2 - - - -
189M SER* 3.2 25.3 + - - -
191M HIS* 3.6 15.8 - - + -
192M PRO* 3.4 27.1 - - + -
201M PHE* 3.8 23.0 - + - -
204M SER* 5.5 0.4 + - - -
206M PRO* 4.6 14.6 - - + +
207M PHE* 4.8 3.6 - + - -
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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