Contacts of the strand formed by residues 156 - 165 (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 GLN 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.4 16.8 - - + -
39A PRO* 3.1 34.6 - - - +
147A ARG* 3.1 8.9 - - - +
148A TRP 3.0 22.3 + - - +
153A ASN* 3.7 19.0 + - - +
154A PRO* 2.8 25.6 + - - +
155A LEU* 1.3 79.2 - - - +
157A PRO* 1.3 79.2 - - + +
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Residues in contact with PRO 157 (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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37A GLU 3.3 12.4 - - - +
38A TYR* 3.5 9.5 - - - -
145A VAL* 4.2 14.8 - - + -
146A VAL 3.8 6.1 - - - +
147A ARG* 3.8 24.0 - - + +
156A GLN* 1.3 92.9 - - + +
158A LEU* 1.3 59.7 + - - +
159A LEU 5.1 0.7 - - - +
160A LYS* 4.5 17.9 - - - +
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Residues in contact with LEU 158 (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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35A GLU 3.8 0.5 - - - +
36A GLY* 3.1 6.6 - - - -
37A GLU 2.9 33.6 + - - +
38A TYR* 3.7 35.4 - - + -
41A ILE* 4.5 11.4 - - + -
44A PHE* 5.1 6.7 - - + -
146A VAL* 2.8 14.5 + - + +
148A TRP* 3.4 55.4 - - + +
156A GLN 3.4 0.4 + - - -
157A PRO* 1.3 75.1 - - - +
159A LEU* 1.4 78.6 + - + +
160A LYS* 6.2 0.7 - - - -
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Residues in contact with LEU 159 (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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35A GLU 3.4 2.7 - - - -
36A GLY* 3.9 14.1 - - - -
44A PHE* 3.9 15.0 - - + -
46A TYR* 3.4 25.6 - - + +
64A GLN* 6.2 0.4 - - - +
144A TYR* 4.0 11.9 - - + +
145A VAL* 3.4 7.4 - - - +
146A VAL* 2.8 51.0 + - + +
157A PRO* 5.8 0.2 - - - -
158A LEU* 1.4 105.1 - - + +
160A LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 160 (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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34A GLY* 3.0 1.9 - - - -
35A GLU* 2.9 49.5 + - + +
46A TYR* 3.8 1.7 + - - -
144A TYR* 3.3 13.9 - - - +
145A VAL* 4.4 14.4 - - + -
157A PRO* 4.5 20.5 - - - +
158A LEU 6.2 0.4 - - - -
159A LEU* 1.3 77.2 - - - +
161A ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 161 (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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33A GLN 3.4 16.2 - - - +
34A GLY* 3.7 5.6 - - - -
48A GLU* 3.5 13.0 - - - +
142A LEU 3.9 0.2 - - - +
143A SER* 3.3 3.8 - - - -
144A TYR* 3.0 61.0 + - + +
160A LYS* 1.3 77.5 - - - +
162A ILE* 1.3 67.1 + - - +
163A LEU* 4.1 6.3 - - + -
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Residues in contact with ILE 162 (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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32A GLY* 3.4 2.3 - - - -
33A GLN* 3.1 27.5 + - - +
138A VAL* 5.1 5.4 - - + -
141A LYS* 3.9 35.2 - - + -
142A LEU 3.3 7.0 - - - +
143A SER* 4.1 14.1 - - - -
161A ALA* 1.3 81.4 - - - +
163A LEU* 1.3 64.7 + - - +
164A ASP* 5.2 0.7 - - - +
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Residues in contact with LEU 163 (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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30A TRP* 3.6 33.3 - - + +
31A ARG 3.6 6.7 - - - -
32A GLY* 3.8 7.0 - - - +
48A GLU* 3.6 32.8 - - + +
50A ILE* 4.0 22.0 - - + -
141A LYS* 3.4 6.3 - - - +
142A LEU* 2.8 48.3 + - + +
144A TYR* 4.1 16.8 - - + -
161A ALA* 4.1 19.1 - - + -
162A ILE* 1.3 82.1 - - - +
164A ASP* 1.3 66.7 + - - +
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Residues in contact with ASP 164 (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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30A TRP* 3.2 3.9 - - - -
31A ARG 2.9 36.8 + - - +
32A GLY* 4.7 0.2 - - - -
141A LYS* 2.8 44.7 + - - +
162A ILE* 5.2 0.9 - - - +
163A LEU* 1.3 74.3 - - - +
165A LYS* 1.3 68.5 + - - +
166A LEU* 3.6 7.0 + - + +
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Residues in contact with LYS 165 (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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25A TYR* 3.9 9.2 - - - +
27A LEU 3.1 29.2 + - - -
28A GLY* 4.0 8.6 - - - -
29A THR 3.7 6.3 - - - +
30A TRP* 3.5 46.1 - - + -
140A GLY 4.5 7.6 + - - +
164A ASP* 1.3 76.3 - - - +
166A LEU* 1.3 75.1 + - - +
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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