Contacts of the strand formed by residues 141 - 150 (chain A) in PDB entry 3WJG
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 LYS 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A TRP* 4.2 0.2 - - - -
137A LEU* 3.2 7.4 - - - -
138A VAL* 2.8 40.2 + - + +
139A ASP* 4.0 13.6 + - + +
140A GLY* 1.3 80.3 - - - +
142A LEU* 1.3 61.9 + - - +
143A SER 3.6 0.3 + - - -
162A ILE* 3.9 24.2 - - + -
163A LEU 3.4 10.8 - - - +
164A ASP* 2.8 36.1 + - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 5.1 1.8 - - + -
26A LEU* 3.9 20.6 - - + -
30A TRP* 3.5 34.3 - - + -
50A ILE* 4.3 18.6 - - + -
52A PHE* 4.0 26.2 - - + -
135A PHE* 4.1 30.1 - - + -
136A GLU 3.9 10.8 - - - +
137A LEU* 4.3 7.9 - - + +
141A LYS* 1.3 71.0 - - - +
143A SER* 1.3 62.2 + - - +
144A TYR* 5.6 0.4 - - + -
162A ILE* 3.3 2.8 - - - -
163A LEU* 2.8 47.4 + - + +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 3.2 6.8 - - - +
136A GLU* 2.8 55.0 + - - +
138A VAL* 3.8 21.0 - - - +
141A LYS 3.6 0.2 + - - -
142A LEU* 1.3 74.8 - - - +
144A TYR* 1.3 64.2 + - - +
161A ALA 3.3 9.4 - - - -
162A ILE* 4.1 12.8 - - - +
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Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 2.8 16.3 + - - -
48A GLU* 2.4 43.2 + - - -
50A ILE* 4.4 4.7 - - + -
62A TYR* 6.2 0.2 - - - -
64A GLN* 4.7 1.7 + - - -
133A ARG* 6.3 0.4 - - + -
134A GLU 3.0 15.3 - - - +
135A PHE* 3.7 30.1 - + + -
142A LEU* 5.6 0.9 - - + -
143A SER* 1.3 77.6 - - - +
145A VAL* 1.3 71.8 + - - +
146A VAL* 3.8 28.5 - - + -
159A LEU* 4.0 18.6 - - + +
160A LYS* 3.3 5.0 - - - +
161A ALA* 3.0 45.1 + - + +
163A LEU* 4.1 11.2 - - + -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER 3.8 1.0 - - - +
133A ARG* 3.5 2.4 - - - -
134A GLU* 2.9 36.0 + - + +
144A TYR* 1.3 80.4 - - - +
146A VAL* 1.3 70.1 + - - +
147A ARG* 3.5 41.9 + - + +
157A PRO* 4.2 14.4 - - + -
159A LEU 3.4 9.6 - - - +
160A LYS* 4.4 16.8 - - + -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ILE* 4.0 8.7 - - + -
132A SER 3.3 9.2 - - - +
133A ARG* 4.1 31.4 - - + +
144A TYR* 3.8 26.4 - - + -
145A VAL* 1.3 73.0 - - - +
147A ARG* 1.3 61.4 + - - +
148A TRP* 3.8 27.4 - - + +
157A PRO* 3.8 2.3 - - - +
158A LEU* 2.8 23.7 + - + -
159A LEU* 2.8 38.2 + - + +
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ILE* 3.2 4.9 - - - -
132A SER* 2.9 48.4 + - - +
134A GLU* 3.6 30.1 + - - +
145A VAL* 3.5 31.7 + - + +
146A VAL* 1.3 74.9 - - - +
148A TRP* 1.3 64.3 + - - +
155A LEU* 3.7 21.3 - - + -
156A GLN* 3.1 26.0 - - - +
157A PRO* 3.7 20.0 - - + +
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Residues in contact with TRP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 2.7 35.6 + + + +
41A ILE* 6.2 4.7 - - + -
100A LEU* 4.1 22.9 - - + -
102A GLU* 5.4 1.5 + - - -
128A VAL* 3.1 35.2 - - + -
130A GLU 3.4 4.0 - - - +
131A ILE* 3.5 27.8 - - + +
146A VAL* 3.8 14.6 - - + +
147A ARG* 1.3 85.2 - - - +
149A SER* 1.3 58.8 + - - +
150A THR* 5.3 6.3 - - + -
155A LEU* 3.5 5.5 - - - -
156A GLN 3.0 23.7 + - - +
158A LEU* 3.4 32.8 - - + +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.6 0.2 - - - -
128A VAL* 3.4 9.7 - - - +
129A LYS* 2.9 23.6 + - - +
130A GLU* 2.7 50.0 + - - +
148A TRP* 1.3 72.6 - - - +
150A THR* 1.3 68.8 + - - +
153A ASN 3.2 13.0 - - - -
154A PRO* 3.9 1.6 - - - -
155A LEU* 3.5 22.9 - - - +
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.9 18.4 - - + +
127A LYS* 3.2 28.9 - - + +
128A VAL* 4.4 7.4 - - + -
129A LYS* 3.8 7.7 - - - +
148A TRP* 5.3 3.8 - - + -
149A SER* 1.3 84.0 - - - +
151A THR* 1.3 66.3 + - - +
152A THR* 3.1 4.9 + - - -
153A ASN* 2.8 51.9 + - - +
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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