Contacts of the strand formed by residues 124 - 130 (chain B) in PDB entry 1W5A
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 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 2.9 3.7 + - - +
40B ILE* 3.4 18.3 - - + +
41B THR 3.0 24.4 + - - +
122B SER* 3.3 1.2 - - - -
123B ASP* 1.3 81.2 - - - +
125B VAL* 1.3 68.1 + - - +
126B PHE* 3.4 39.7 - - + -
152B ALA* 4.2 0.2 - - - -
153B LEU* 3.3 38.8 - - + +
155B VAL* 3.6 16.6 - - + -
226B ILE* 3.7 20.2 - - + -
236B PHE* 4.0 18.2 - - + -
239B VAL* 4.3 0.4 - - + -
243B MET* 3.6 15.9 - - - -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.3 9.9 - - - +
43B VAL* 4.0 22.4 - - + -
119B ILE* 4.3 17.0 - - + +
122B SER* 3.6 22.9 - - - +
124B MET* 1.3 80.1 - - - +
126B PHE* 1.3 68.9 + - - +
127B ILE* 3.9 11.7 + - + +
143B VAL* 4.9 1.1 - - + -
147B SER* 3.3 30.1 - - - +
150B ILE* 5.0 0.2 - - + -
152B ALA* 3.9 5.8 - - + -
153B LEU 2.9 9.5 + - - +
154B THR* 3.8 1.0 - - - -
155B VAL* 2.9 27.9 + - - +
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Residues in contact with PHE 126 (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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40B ILE* 4.0 19.1 - - + -
41B THR 2.8 10.0 + - - +
42B VAL* 3.4 19.1 - - + +
43B VAL* 2.6 35.5 + - - +
124B MET* 3.4 43.5 - - + -
125B VAL* 1.3 76.2 - - - +
127B ILE* 1.3 57.9 + - - +
128B THR* 4.0 1.1 - - - -
155B VAL* 3.0 21.1 - - + -
157B VAL* 4.4 14.6 - - + -
219B VAL* 4.9 5.8 - - + -
222B LEU* 3.8 32.3 - - + -
223B VAL* 3.8 35.7 - - + -
226B ILE* 4.5 5.6 - - + -
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Residues in contact with ILE 127 (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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43B VAL* 3.4 4.0 - - + +
45B CYS* 4.2 17.9 - - - -
125B VAL* 4.2 9.9 - - + +
126B PHE* 1.3 75.0 - - - +
128B THR* 1.3 62.5 + - - +
129B CYS* 5.8 0.2 - - - -
140B ALA* 4.0 26.7 - - + +
143B VAL* 4.0 16.6 - - + +
144B ALA* 3.2 48.0 - - + +
147B SER* 5.0 0.2 - - - -
154B THR* 3.9 12.8 - - + -
155B VAL 2.8 13.5 + - - +
156B ALA* 3.1 16.7 - - + +
157B VAL 2.8 25.6 + - - +
158B VAL* 4.1 3.0 - - + +
180B LEU* 5.2 0.7 - - + -
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Residues in contact with THR 128 (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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42B VAL* 4.4 14.6 - - + -
43B VAL 2.8 17.2 + - - +
44B GLY* 3.2 9.2 - - - -
45B CYS* 3.1 19.9 + - - -
49B GLY* 3.8 1.4 - - - +
52B THR* 4.2 25.3 + - + +
53B ILE* 4.8 1.6 - - + -
126B PHE* 4.0 1.5 + - - -
127B ILE* 1.3 76.3 - - - +
129B CYS* 1.3 67.2 + - - +
157B VAL* 2.9 17.0 + - - -
215B LEU* 3.5 19.9 - - - +
219B VAL* 3.9 15.1 - - + +
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Residues in contact with CYS 129 (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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45B CYS* 3.3 25.8 - - + +
48B ALA* 4.8 1.3 - - - -
49B GLY* 4.0 8.3 - - - -
127B ILE* 5.8 0.2 - - - -
128B THR* 1.3 81.9 + - - +
130B GLY* 1.3 61.2 + - - +
131B LEU* 3.5 30.3 - - - -
136B GLY* 3.9 22.2 - - - -
140B ALA* 4.1 9.0 - - + -
157B VAL 3.5 2.2 + - - +
158B VAL* 3.4 15.9 - - - +
159B THR* 3.3 22.0 + - - +
215B LEU* 4.8 5.0 - - - +
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Residues in contact with GLY 130 (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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45B CYS 4.7 0.4 + - - -
48B ALA* 3.9 14.7 - - - +
49B GLY 4.5 0.6 - - - +
129B CYS* 1.3 79.8 - - - +
131B LEU* 1.3 67.1 + - - -
132B GLY 3.8 0.3 + - - -
133B GLY 4.2 1.6 + - - -
136B GLY* 4.7 0.2 - - - -
137B THR* 4.5 2.4 + - - -
159B THR* 3.3 17.0 - - - -
215B LEU* 5.7 0.4 - - - -
500B GTP 3.1 37.9 + - - +
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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