Contacts of the strand formed by residues 163 - 168 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60G VAL* 4.5 1.3 - - + -
61G ARG 3.8 10.3 - - - +
62G VAL 4.2 0.9 - - - +
63G LEU* 3.8 28.5 - - + +
153G ILE* 5.3 2.7 - - + +
156G LEU* 4.0 40.8 - - + +
157G ALA* 4.3 3.6 - - - +
159G ARG* 4.0 12.8 - - - +
161G ALA 3.6 2.6 + - - +
162G PRO* 1.3 76.2 - - - +
164G VAL* 1.3 70.5 + - - +
165G ALA* 4.5 2.9 - - + +
179G LEU* 4.3 16.4 - - + -
183G ASN* 3.6 6.9 + - - +
184G CYS* 3.2 28.7 - - + +
185G VAL 3.0 25.6 + - - +
217G MET* 4.3 0.5 - - - +
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Residues in contact with VAL 164 (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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61G ARG 3.0 11.9 + - - +
62G VAL* 3.0 13.1 - - + +
63G LEU 2.8 22.0 + - - -
163G LEU* 1.3 73.5 - - - +
165G ALA* 1.3 66.9 + - - +
166G ILE* 4.6 4.3 - - + -
185G VAL 3.3 8.3 - - - +
187G ILE* 5.0 3.4 - - + -
210G ALA* 3.7 33.2 - - + +
213G LEU* 3.7 25.1 - - + -
214G LEU* 3.7 15.7 - - + -
217G MET* 3.5 29.2 - - + -
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Residues in contact with ALA 165 (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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63G LEU* 3.3 24.0 - - + +
163G LEU* 4.0 2.2 - - + -
164G VAL* 1.3 74.2 - - - +
166G ILE* 1.3 61.4 + - - +
167G LEU* 3.6 16.3 - - + +
179G LEU* 3.4 31.9 - - + -
185G VAL 3.0 7.6 + - - +
186G ALA* 3.2 3.6 - - + -
187G ILE* 3.1 24.1 + - - +
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Residues in contact with ILE 166 (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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62G VAL* 4.2 16.2 - - + -
63G LEU 2.7 16.7 + - - +
64G ILE* 3.2 34.2 - - + +
65G VAL* 3.9 14.6 + - - +
164G VAL* 4.6 1.6 - - + -
165G ALA* 1.3 74.8 - - - +
167G LEU* 1.3 61.1 + - - +
168G TRP* 3.4 44.3 + - + +
187G ILE* 3.6 34.3 - - + +
206G PRO* 4.6 7.4 - - + +
207G PHE* 5.3 4.3 - - + -
210G ALA* 4.5 10.3 - - + -
224G TRP* 5.4 1.8 - - + -
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Residues in contact with LEU 167 (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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63G LEU* 5.4 0.7 - - + -
65G VAL* 4.3 12.1 - - + -
165G ALA* 3.6 30.3 - - + +
166G ILE* 1.3 79.6 - - - +
168G TRP* 1.3 61.8 + - - +
169G GLY 3.8 2.9 + - - +
172G ALA* 3.5 36.8 - - + +
173G SER* 4.0 16.2 - - - +
175G LEU* 4.8 2.7 - - + -
176G LYS* 4.2 19.3 - - + +
179G LEU* 4.8 4.9 - - + -
186G ALA* 4.4 11.7 - - + -
187G ILE 2.9 12.4 + - - +
188G GLU* 3.4 35.5 - - + +
189G SER 3.5 5.2 + - - +
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Residues in contact with TRP 168 (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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64G ILE* 3.9 11.4 - - + -
65G VAL 4.8 6.0 + - - +
67G GLN* 5.1 3.5 + - - -
81G PHE* 3.5 33.3 - + + -
97G ILE* 3.3 44.2 - - + -
118G TRP* 5.7 1.3 - + - -
166G ILE* 3.4 40.5 + - + +
167G LEU* 1.3 72.6 - - - +
169G GLY* 1.3 65.0 + - - +
172G ALA* 3.5 13.0 + - - +
187G ILE* 5.4 1.7 - - + +
189G SER* 3.3 23.8 + - - -
191G HIS* 3.6 15.4 - - + -
192G PRO* 3.5 28.9 - - + -
201G PHE* 3.6 22.4 - + - -
206G PRO* 4.4 17.1 - - + +
207G PHE* 4.7 6.7 - + - -
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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