Contacts of the strand formed by residues 128 - 139 (chain D) in PDB entry 2W7U
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 MET 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D GLU* 3.5 6.8 - - - +
7D ILE* 2.8 54.3 + - + +
10D ALA* 3.8 11.4 - - + -
15D TYR* 3.5 50.0 - - + +
18D VAL* 4.1 12.6 - - - +
55D HIS 4.0 10.3 + - - +
56D SER* 4.7 2.3 - - - +
57D SER 5.5 0.2 - - - +
116D ILE* 3.7 23.6 - - + -
117D GLY 3.7 10.1 - - - +
118D TYR* 3.7 27.6 - - + -
126D TYR 3.9 1.6 + - - -
127D LYS* 1.3 73.3 - - - +
129D PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 129 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D VAL* 3.7 26.9 - - + -
5D LYS 3.6 2.2 - - - +
6D GLU* 3.7 31.9 - - + -
7D ILE* 4.5 3.8 - - - -
115D VAL 3.7 1.4 - - - +
116D ILE* 3.4 5.8 - - - +
117D GLY 3.1 31.7 + - - -
119D PRO* 3.7 39.3 - - + -
124D THR* 4.8 11.2 - - + -
127D LYS* 3.3 51.1 - - + -
128D MET* 1.3 73.2 - - - +
130D GLU* 1.3 59.5 + - - +
131D SER* 5.7 0.9 - - - -
153D ASN* 5.4 0.2 - - - +
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Residues in contact with GLU 130 (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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3D ASN 3.7 1.7 - - - +
4D VAL* 3.4 4.8 - - - -
5D LYS* 2.9 44.4 + - + +
7D ILE* 3.5 22.2 - - + +
15D TYR* 3.2 30.6 + - - -
114D SER* 3.4 28.6 + - - -
115D VAL 3.5 2.5 - - - -
116D ILE* 3.8 18.3 - - + +
129D PHE* 1.3 73.3 - - - +
131D SER* 1.3 63.8 + - - +
132D THR* 4.8 8.0 - - + +
163D HIS* 5.6 4.7 + - - -
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Residues in contact with SER 131 (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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3D ASN 3.6 4.7 + - - -
4D VAL* 3.7 12.9 - - - +
114D SER* 3.5 0.4 - - - -
115D VAL* 2.6 49.3 + - - +
129D PHE* 5.6 1.1 - - - -
130D GLU* 1.3 75.5 - - - +
132D THR* 1.3 62.9 + - - +
147D ALA* 3.8 4.4 - - - +
148D TYR* 2.9 48.2 + - - +
153D ASN* 5.9 1.6 - - - -
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Residues in contact with THR 132 (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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1D GLU* 3.5 23.3 + - - +
3D ASN* 2.9 40.4 + - - +
112D ARG* 4.0 12.7 + - - +
113D ILE 3.4 12.8 - - - +
114D SER* 4.1 13.5 - - - -
130D GLU* 4.8 9.2 - - + +
131D SER* 1.3 78.8 + - - +
133D GLY* 1.3 58.6 + - - +
147D ALA* 3.7 9.4 - - - +
148D TYR 4.6 0.2 + - - -
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Residues in contact with GLY 133 (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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1D GLU* 3.5 11.9 - - - -
112D ARG* 3.6 10.1 - - - +
113D ILE* 2.9 34.8 + - - +
132D THR* 1.3 75.9 - - - +
134D THR* 1.3 62.8 + - - -
146D ASP* 3.4 11.9 - - - -
147D ALA* 3.9 12.0 - - - +
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Residues in contact with THR 134 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D GLU* 4.0 2.3 + - - -
110D LYS* 3.7 32.8 - - + +
111D ASP 3.4 16.6 - - - +
112D ARG* 3.4 22.5 + - - -
113D ILE* 4.0 1.1 - - - +
133D GLY* 1.3 75.7 - - - +
135D ILE* 1.3 66.6 + - - +
136D ASN* 3.5 8.8 + - - +
145D PHE* 3.3 5.3 - - - -
146D ASP* 2.8 41.7 + - - +
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Residues in contact with ILE 135 (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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107D ALA* 3.9 28.9 - - + -
108D LYS 3.9 14.6 - - - +
109D VAL* 3.5 4.0 - - - +
110D LYS* 2.8 31.1 + - - +
111D ASP* 3.1 13.6 + - + +
113D ILE* 3.8 32.1 - - + -
134D THR* 1.3 70.6 - - - +
136D ASN* 1.3 63.3 + - - +
137D HIS 4.0 5.6 - - - +
138D ILE* 3.7 30.7 - - + -
143D MET* 5.0 11.7 - - + -
144D GLU 3.5 12.1 - - - +
145D PHE* 4.2 6.1 - - + -
158D VAL* 5.8 0.4 - - + -
166D ILE* 4.6 7.0 - - + -
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Residues in contact with ASN 136 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D VAL* 3.4 16.9 - - - +
110D LYS* 5.8 4.2 - - - +
134D THR* 3.6 12.5 + - - +
135D ILE* 1.3 76.5 + - - +
137D HIS* 1.3 64.2 + - + +
144D GLU* 2.8 25.2 + - - +
145D PHE* 4.0 2.9 - - - -
146D ASP* 3.3 41.8 + - - +
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Residues in contact with HIS 137 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173B SER* 4.6 1.0 + - - -
180B LYS* 3.9 36.6 - - + +
109D VAL* 4.7 3.4 - - - -
135D ILE* 3.6 2.8 - - - +
136D ASN* 1.3 83.6 + - + +
138D ILE* 1.3 77.0 + - - +
139D SER* 3.5 20.9 - - - -
142D PHE* 3.9 23.6 - + - -
143D MET* 3.2 3.8 - - - +
144D GLU* 2.7 44.5 + - + +
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Residues in contact with ILE 138 (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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107D ALA* 3.4 32.3 - - + +
108D LYS* 3.7 23.1 - - - +
109D VAL* 4.0 13.6 - - + +
135D ILE* 3.7 16.2 - - + -
137D HIS* 1.3 85.7 + - - +
139D SER* 1.3 65.2 + - - +
140D GLY 4.6 4.3 - - - +
142D PHE 3.5 8.5 - - - +
143D MET* 4.2 9.0 - - + -
185D TYR* 4.2 31.4 - - + -
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Residues in contact with SER 139 (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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173B SER* 3.2 25.0 + - - +
174B GLY 4.4 2.1 + - - -
137D HIS* 3.5 21.2 - - - -
138D ILE* 1.3 73.4 - - - +
140D GLY* 1.3 60.9 + - - +
141D THR* 3.1 1.2 + - - +
142D PHE* 2.8 34.6 + - - +
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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