Contacts of the strand formed by residues 116 - 122 (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 TRP 116 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103G LEU* 5.1 2.2 - - + -
104G PHE* 3.5 1.0 - - - -
105G SER* 2.8 46.6 + - - +
114G SER* 2.9 41.4 + - - +
115G ASN* 1.3 75.8 - - - +
117G TRP* 1.3 62.3 + - - +
137G TYR* 4.1 31.7 + + + -
142G PRO* 3.5 42.6 - - + -
143G PHE 3.2 22.2 - - - -
144G ARG* 3.5 46.0 - - + -
145G GLY 4.2 0.4 - - - +
164G MET* 3.6 7.7 - - - +
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Residues in contact with TRP 117 (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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103G LEU* 3.1 15.5 - - - +
116G TRP* 1.3 75.1 - - - +
118G ASN* 1.3 63.3 + - - +
119G VAL* 3.4 34.8 - - + -
142G PRO* 3.3 4.3 - - - +
143G PHE* 2.9 78.7 + + + +
144G ARG 4.1 6.9 + - - -
145G GLY 4.5 0.2 - - - -
150G HIS* 3.7 15.1 - + + -
160G SER* 4.9 3.4 - - - -
161G ARG 4.5 0.4 - - - -
162G GLY* 3.4 48.5 - - - -
164G MET* 3.4 40.6 - - + +
172G LEU* 3.7 17.7 - - + -
174G ILE* 4.0 11.9 - - + -
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Residues in contact with ASN 118 (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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101G ALA 4.5 0.2 - - - -
102G VAL* 3.3 7.0 - - - +
103G LEU* 2.9 48.9 + - + +
117G TRP* 1.3 77.2 - - - +
119G VAL* 1.3 80.7 + - - +
120G ARG* 4.4 1.1 - - - +
136G LEU* 2.8 37.1 + - + +
140G ARG* 3.7 18.6 + - - +
142G PRO* 3.6 21.9 - - + +
143G PHE* 4.6 2.8 - - - -
152G ARG* 3.4 22.4 + - - -
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Residues in contact with VAL 119 (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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100G LEU* 4.0 20.2 - - + -
101G ALA 3.5 6.7 - - - +
102G VAL* 4.3 6.7 - - + -
117G TRP* 3.4 29.4 - - + -
118G ASN* 1.3 92.0 + - - +
120G ARG* 1.3 67.1 + - - +
143G PHE* 5.1 2.0 - - + -
152G ARG* 4.1 11.6 + - - -
154G LEU* 3.3 18.2 - - + +
160G SER* 3.6 28.5 + - - +
174G ILE* 3.8 21.5 - - + -
176G VAL* 4.7 5.4 - - + -
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Residues in contact with ARG 120 (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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99G THR 3.8 0.3 - - - +
100G LEU* 3.9 2.5 - - - +
101G ALA* 3.0 34.0 + - - +
118G ASN* 4.4 1.4 + - - +
119G VAL* 1.3 77.7 + - - +
121G VAL* 1.3 75.6 + - - +
122G TYR* 3.9 21.5 - - + -
136G LEU* 3.5 22.4 - - + +
140G ARG* 2.8 62.2 + - - +
152G ARG* 2.5 43.2 - - - +
153G GLY 4.8 5.5 + - - -
154G LEU* 3.9 10.6 + - - +
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Residues in contact with VAL 121 (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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94G MET* 4.0 16.2 - - + -
98G ASN* 4.2 1.6 - - + -
99G THR 3.4 8.3 - - - +
100G LEU* 4.0 13.0 - - + -
120G ARG* 1.3 85.2 - - - +
122G TYR* 1.3 71.1 + - - +
123G LYS 4.2 0.2 + - - -
154G LEU* 3.6 41.7 + - + +
156G TYR* 3.3 46.2 + - + -
158G LEU* 4.3 12.3 - - + -
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Residues in contact with TYR 122 (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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98G ASN* 3.1 7.8 - - - +
99G THR* 2.8 45.1 + - + +
101G ALA* 3.9 28.0 - - + -
120G ARG* 3.9 17.4 - - + +
121G VAL* 1.3 78.4 - - - +
123G LYS* 1.3 60.6 + - - +
124G GLY 4.4 0.2 - - - -
126G LYS* 3.9 32.5 - - + -
132G MET* 4.0 20.3 - - + +
135G GLU* 2.6 43.3 + - - +
136G LEU* 3.8 14.7 - - + +
140G ARG* 4.3 19.2 + - - -
156G TYR* 4.5 0.9 - - - -
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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