Contacts of the strand formed by residues 158 - 164 (chain G) in PDB entry 3ZWG
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 158 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41G SER* 3.5 43.5 - - - +
43G LYS* 4.6 10.1 - - + -
94G MET* 3.7 37.7 - - + -
100G LEU* 5.4 0.2 - - + -
121G VAL* 4.3 11.4 - - + -
153G GLY* 3.9 1.2 - - - -
154G LEU* 2.9 31.5 + - + -
155G GLY 2.8 11.7 + - - +
156G TYR* 3.7 13.0 - - + +
157G GLY* 1.3 85.5 - - - +
159G LYS* 1.3 62.6 + - - +
176G VAL* 4.3 9.6 - - + -
177G THR 3.5 7.2 - - - +
178G LYS* 4.6 2.0 - - + -
179G ALA* 3.7 6.2 - - - +
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Residues in contact with LYS 159 (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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151G SER* 5.2 14.4 - - - -
152G ARG 3.7 13.2 - - - +
153G GLY* 3.9 8.5 - - - +
154G LEU* 4.0 6.7 - - - +
158G LEU* 1.3 75.4 - - - +
160G SER* 1.3 60.9 + - - +
161G ARG* 6.2 4.0 - - + +
175G HIS 3.8 1.0 - - - +
176G VAL* 3.6 2.6 - - - +
177G THR* 3.0 53.3 + - - +
178G LYS 3.8 5.1 + - - -
179G ALA* 3.6 29.0 + - + +
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Residues in contact with SER 160 (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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117G TRP* 4.9 4.3 - - - -
119G VAL* 3.6 42.3 + - - +
143G PHE* 5.1 3.6 - - - -
150G HIS 3.6 1.5 - - - +
151G SER* 3.1 6.5 - - - -
152G ARG* 2.9 47.8 + - - +
154G LEU* 3.8 11.9 - - - +
159G LYS* 1.3 75.2 - - - +
161G ARG* 1.3 60.2 + - - +
162G GLY 4.3 0.2 - - - -
174G ILE* 4.8 2.0 - - - -
175G HIS 3.7 4.7 - - - -
176G VAL* 4.6 5.6 - - - +
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Residues in contact with ARG 161 (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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117G TRP* 4.5 1.3 - - - -
149G TRP* 3.3 44.8 - - + -
150G HIS 3.5 4.0 - - - +
151G SER* 3.5 20.6 - - - +
159G LYS* 6.2 4.5 - - + +
160G SER* 1.3 74.4 - - - +
162G GLY* 1.3 59.7 + - - +
173G GLU 3.9 0.3 - - - +
174G ILE* 3.2 3.1 - - - +
175G HIS* 2.6 87.5 + - - +
177G THR* 5.9 2.9 - - + +
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Residues in contact with GLY 162 (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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117G TRP* 3.4 26.5 - - - -
148G GLY 3.9 0.5 - - - +
149G TRP* 3.3 8.7 - - - -
150G HIS 2.9 33.5 + - - -
161G ARG* 1.3 77.3 - - - +
163G PHE* 1.3 60.0 + - - -
173G GLU 3.0 11.0 - - - -
174G ILE* 4.0 3.8 - - - -
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Residues in contact with PHE 163 (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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117G TRP* 4.1 2.4 - - - -
147G ASN* 3.4 54.7 - - + -
148G GLY* 3.5 21.1 - - - -
149G TRP* 3.6 44.9 - + + -
162G GLY* 1.3 73.2 - - - -
164G MET* 1.3 69.1 - - - +
165G ASN* 4.4 4.0 - - + -
171G ILE* 3.5 8.1 - - + +
172G LEU* 3.3 9.1 - - - +
173G GLU* 2.8 35.2 + - + +
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Residues in contact with MET 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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33G ILE* 3.7 29.8 - - + -
104G PHE* 4.8 1.8 - - + -
105G SER 4.1 2.0 - - - +
106G VAL* 3.8 17.9 - - + -
115G ASN* 4.1 12.8 - - - -
116G TRP* 3.6 38.1 - - - +
117G TRP* 3.4 28.1 - - + +
145G GLY* 3.3 9.8 - - - -
146G ASP* 3.4 0.7 + - - +
147G ASN* 3.1 23.6 + - - -
148G GLY 4.4 3.5 + - - -
163G PHE* 1.3 81.8 - - - +
165G ASN* 1.3 70.7 + - - +
170G ALA* 4.0 8.3 - - + -
171G ILE 3.4 11.4 - - - +
172G LEU* 4.0 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