Contacts of the strand formed by residues 116 - 122 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D LEU* 5.1 1.8 - - + -
104D PHE* 3.5 1.0 - - - -
105D SER* 2.7 46.1 + - - +
114D SER* 2.9 40.6 + - - +
115D ASN* 1.3 76.8 - - - +
117D TRP* 1.3 63.0 + - - +
137D TYR* 4.0 33.6 + + + -
142D PRO* 3.6 41.1 - - + -
143D PHE 3.3 9.0 - - - -
144D ARG* 3.5 60.6 - - + -
145D GLY 4.2 0.4 - - - +
164D MET* 3.7 7.1 - - - +
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Residues in contact with TRP 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 3.1 16.6 - - - +
104D PHE* 4.7 0.2 - - - -
116D TRP* 1.3 75.7 - - - +
118D ASN* 1.3 63.8 + - - +
119D VAL* 3.4 34.5 - - + -
142D PRO* 3.3 3.7 - - - +
143D PHE* 2.9 81.2 + + + +
144D ARG 4.0 6.3 + - - -
150D HIS* 3.7 16.4 - + + -
160D SER* 4.9 3.8 - - - -
161D ARG 4.5 0.2 - - - -
162D GLY* 3.4 47.3 - - - -
164D MET* 3.4 40.8 - - + +
172D LEU* 3.8 16.2 - - + -
174D ILE* 4.1 11.9 - - + -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA 4.5 0.4 - - - -
102D VAL* 3.3 7.0 - - - +
103D LEU* 2.9 49.4 + - + +
117D TRP* 1.3 75.8 - - - +
119D VAL* 1.3 81.0 + - - +
120D ARG* 4.4 0.8 + - - +
136D LEU* 2.8 36.3 + - + +
140D ARG* 3.7 21.0 + - - +
142D PRO* 3.6 19.1 - - + +
143D PHE* 4.6 2.2 - - - -
152D ARG* 3.4 21.7 + - - -
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 4.1 20.2 - - + -
101D ALA 3.5 6.1 - - - +
102D VAL* 4.2 7.0 - - + -
117D TRP* 3.4 27.8 - - + -
118D ASN* 1.3 92.2 + - - +
120D ARG* 1.3 64.8 + - - +
143D PHE* 5.1 2.7 - - + -
152D ARG* 4.2 11.4 + - - -
154D LEU* 3.2 18.7 - - + +
160D SER* 3.6 28.3 + - - +
174D ILE* 3.8 22.9 - - + -
176D VAL* 4.7 4.7 - - + -
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Residues in contact with ARG 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 3.9 2.6 - - - +
101D ALA* 3.0 34.6 + - - +
118D ASN* 4.4 1.6 + - - +
119D VAL* 1.3 76.6 + - - +
121D VAL* 1.3 75.3 + - - +
122D TYR* 3.9 21.3 - - + -
136D LEU* 3.5 22.4 - - + +
140D ARG* 2.8 61.0 + - - +
152D ARG* 2.5 45.1 - - - +
153D GLY 4.8 5.7 + - - -
154D LEU* 3.9 11.3 + - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D MET* 4.1 15.9 - - + -
98D ASN* 4.2 2.2 - - + -
99D THR 3.4 7.6 - - - +
100D LEU* 4.0 13.5 - - + -
120D ARG* 1.3 84.0 - - - +
122D TYR* 1.3 71.3 + - - +
154D LEU* 3.6 43.5 + - + +
156D TYR* 3.3 45.7 + - + -
158D LEU* 4.4 12.1 - - + -
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ASN* 3.1 7.3 - - - +
99D THR* 2.8 46.7 + - + +
101D ALA* 3.9 28.9 - - + -
120D ARG* 3.9 18.2 - - + +
121D VAL* 1.3 80.1 - - - +
123D LYS* 1.3 61.0 + - - +
126D LYS* 3.9 33.7 - - + -
132D MET* 4.0 20.5 - - + +
135D GLU* 2.7 41.0 + - - +
136D LEU* 3.8 14.1 - - + +
140D ARG* 4.3 19.2 + - - -
156D TYR* 4.5 0.7 - - - -
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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