Contacts of the strand formed by residues 116 - 122 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LEU* 5.1 2.2 - - + -
104B PHE* 3.5 0.3 - - - -
105B SER* 2.8 45.3 + - - +
114B SER* 2.9 41.5 + - - +
115B ASN* 1.3 76.6 - - - +
117B TRP* 1.3 63.9 + - - +
137B TYR* 4.0 30.9 + + + -
142B PRO* 3.5 42.0 - - + -
143B PHE 3.3 22.4 - - - -
144B ARG* 3.5 46.0 - - + -
145B GLY 4.2 0.7 - - - +
164B MET* 3.5 8.4 - - - +
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Residues in contact with TRP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.2 15.9 - - - +
116B TRP* 1.3 75.8 - - - +
118B ASN* 1.3 69.5 + - - +
119B VAL* 3.4 34.5 - - + -
142B PRO* 3.2 4.8 - - - +
143B PHE* 2.9 78.4 + + + +
144B ARG 4.1 6.7 + - - -
150B HIS* 3.7 16.2 - + + -
160B SER* 5.0 3.4 - - - -
161B ARG 4.5 0.2 - - - -
162B GLY* 3.3 48.5 - - - -
164B MET* 3.4 40.8 - - + +
172B LEU* 3.7 17.3 - - + -
174B ILE* 4.1 11.9 - - + -
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA 4.4 0.7 - - - -
102B VAL* 3.3 6.2 - - - +
103B LEU* 2.9 48.7 + - + +
117B TRP* 1.3 76.9 - - - +
119B VAL* 1.3 80.2 + - - +
120B ARG* 4.9 0.4 - - - -
136B LEU* 2.8 36.7 + - + +
140B ARG* 3.7 21.0 + - - +
142B PRO* 3.6 18.8 - - + +
143B PHE* 4.6 2.8 - - - -
152B ARG* 3.4 21.8 + - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 4.1 14.1 - - + -
101B ALA 3.5 6.1 - - - +
102B VAL* 4.2 6.7 - - + -
117B TRP* 3.4 28.3 - - + -
118B ASN* 1.3 90.5 + - - +
120B ARG* 1.3 66.2 + - - +
143B PHE* 5.1 2.4 - - + -
152B ARG* 4.2 10.9 + - - -
154B LEU* 3.3 25.0 - - + +
160B SER* 3.7 27.7 + - - +
174B ILE* 3.8 23.8 - - + -
176B VAL* 4.6 5.8 - - + -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B THR 3.8 0.2 - - - +
100B LEU* 3.9 2.6 - - - +
101B ALA* 3.0 33.4 + - - +
118B ASN* 4.3 1.4 + - - +
119B VAL* 1.3 77.5 + - - +
121B VAL* 1.3 76.2 + - - +
122B TYR* 3.9 22.2 - - + -
136B LEU* 3.6 22.9 - - + +
140B ARG* 2.9 62.3 + - - +
152B ARG* 2.5 43.8 - - - +
153B GLY 4.8 6.3 + - - -
154B LEU* 3.9 10.1 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B MET* 4.0 16.6 - - + -
98B ASN* 4.2 1.6 - - + -
99B THR 3.4 8.5 - - - +
100B LEU* 4.0 11.4 - - + -
120B ARG* 1.3 87.8 - - - +
122B TYR* 1.3 70.5 + - - +
154B LEU* 3.6 44.0 + - + +
156B TYR* 3.3 45.2 + - + -
158B LEU* 4.5 11.7 - - + -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASN* 3.1 7.8 - - - +
99B THR* 2.8 44.8 + - + +
101B ALA* 3.9 28.0 - - + -
120B ARG* 3.9 18.0 - - + +
121B VAL* 1.3 78.8 - - - +
123B LYS* 1.3 61.7 + - - +
126B LYS* 3.9 33.7 - - + -
132B MET* 4.0 21.6 - - + +
135B GLU* 2.6 41.2 + - - +
136B LEU* 3.8 15.6 - - + +
140B ARG* 4.3 20.2 + - - -
156B 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