Contacts of the strand formed by residues 116 - 122 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E LEU* 5.1 2.2 - - + -
104E PHE* 3.5 2.1 - - - -
105E SER* 2.7 46.6 + - - +
114E SER* 2.8 41.8 + - - +
115E ASN* 1.3 76.0 - - - +
117E TRP* 1.3 60.5 + - - +
137E TYR* 4.0 30.7 + + + -
142E PRO* 3.5 42.2 - - + -
143E PHE 3.3 22.2 - - - -
144E ARG* 3.5 45.3 - - + -
145E GLY 4.2 0.7 - - - +
164E MET* 3.6 7.8 - - - +
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Residues in contact with TRP 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU* 3.1 15.0 - - - +
104E PHE* 4.7 0.2 - - - -
116E TRP* 1.3 74.5 - - - +
118E ASN* 1.3 62.7 + - - +
119E VAL* 3.4 33.4 - - + -
142E PRO* 3.2 5.1 - - - +
143E PHE* 2.9 80.5 + + + +
144E ARG 4.0 7.4 + - - -
150E HIS* 3.7 16.2 - + + -
160E SER* 4.9 3.6 - - - -
161E ARG 4.6 0.4 - - - -
162E GLY* 3.4 47.8 - - - -
164E MET* 3.5 36.3 - - + +
172E LEU* 3.8 21.5 - - + -
174E ILE* 4.1 12.6 - - + -
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Residues in contact with ASN 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E ALA 4.5 0.4 - - - -
102E VAL* 3.3 6.3 - - - +
103E LEU* 2.9 48.3 + - + +
117E TRP* 1.3 77.7 - - - +
119E VAL* 1.3 81.1 + - - +
120E ARG* 4.9 0.4 - - - -
136E LEU* 2.7 36.5 + - + +
140E ARG* 3.7 21.2 + - - +
142E PRO* 3.6 19.8 - - + +
143E PHE* 4.6 2.6 - - - -
152E ARG* 3.4 21.0 + - - -
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Residues in contact with VAL 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LEU* 4.0 19.7 - - + -
101E ALA 3.5 5.8 - - - +
102E VAL* 4.2 6.7 - - + -
117E TRP* 3.4 27.6 - - + -
118E ASN* 1.3 92.9 + - - +
120E ARG* 1.3 66.3 + - - +
143E PHE* 5.1 2.4 - - + -
152E ARG* 4.1 11.1 + - - -
154E LEU* 3.3 19.4 - - + +
160E SER* 3.6 29.1 + - - +
174E ILE* 3.8 23.6 - - + -
176E VAL* 4.7 5.4 - - + -
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Residues in contact with ARG 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LEU* 3.9 2.6 - - - +
101E ALA* 3.0 34.6 + - - +
118E ASN* 4.4 1.4 + - - -
119E VAL* 1.3 76.5 + - - +
121E VAL* 1.3 76.3 + - - +
122E TYR* 3.9 21.9 + - + -
136E LEU* 3.5 22.6 - - + +
140E ARG* 2.8 61.9 + - - +
152E ARG* 2.5 44.4 - - - +
153E GLY 4.8 6.5 + - - -
154E LEU* 3.9 11.0 + - - +
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E MET* 4.0 16.4 - - + -
98E ASN* 4.2 1.3 - - + -
99E THR 3.4 7.6 - - - +
100E LEU* 4.0 13.0 - - + -
120E ARG* 1.3 86.2 - - - +
122E TYR* 1.3 72.1 + - - +
154E LEU* 3.6 42.6 + - + +
156E TYR* 3.3 46.5 + - + -
158E LEU* 4.4 12.8 - - + -
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Residues in contact with TYR 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ASN* 3.1 7.6 - - - +
99E THR* 2.8 43.2 + - + +
101E ALA* 3.9 30.3 - - + -
120E ARG* 3.9 17.3 - - + +
121E VAL* 1.3 78.4 - - - +
123E LYS* 1.3 61.4 + - - +
126E LYS* 3.9 34.1 - - + -
132E MET* 4.0 21.1 - - + +
135E GLU* 2.6 41.0 + - - +
136E LEU* 3.8 14.6 - - + +
140E ARG* 4.3 20.2 + - - -
156E 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