Contacts of the strand formed by residues 124 - 130 (chain A) in PDB entry 1W5B
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS 3.1 6.4 + - - +
40A ILE* 3.4 11.2 - - + -
41A THR 3.0 24.4 + - - +
122A SER* 3.3 1.5 - - - -
123A ASP* 1.3 82.0 - - - +
125A VAL* 1.3 68.9 + - - +
126A PHE* 3.5 34.8 - - + -
152A ALA* 4.2 0.2 - - - -
153A LEU* 3.2 40.8 - - + +
155A VAL* 3.6 13.5 - - + -
226A ILE* 3.8 14.8 - - + -
236A PHE* 4.0 18.2 - - + -
239A VAL* 4.7 0.2 - - + -
243A MET* 3.3 28.0 - - + -
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Residues in contact with VAL 125 (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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41A THR* 3.4 9.6 - - - +
43A VAL* 3.9 23.8 - - + -
119A ILE* 4.4 16.4 - - + +
122A SER* 3.6 21.8 - - - +
124A MET* 1.3 79.4 - - - +
126A PHE* 1.3 66.5 + - - +
127A ILE* 3.9 12.1 + - + -
143A VAL* 5.1 0.7 - - + -
147A SER* 3.1 31.6 - - - +
152A ALA* 3.7 7.2 - - + -
153A LEU 2.8 9.7 + - - +
154A THR* 3.6 1.9 - - - +
155A VAL* 2.8 29.3 + - - +
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Residues in contact with PHE 126 (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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40A ILE* 3.6 25.8 - - + -
41A THR 2.8 10.1 + - - +
42A VAL* 3.4 15.3 - - + +
43A VAL* 2.6 35.2 + - - +
124A MET* 3.5 40.8 - - + -
125A VAL* 1.3 75.4 - - - +
127A ILE* 1.3 57.0 + - - +
128A THR* 6.2 0.9 - - - -
155A VAL* 3.1 24.0 - - + -
157A VAL* 4.5 13.0 - - + -
219A VAL* 5.2 7.6 - - + -
222A LEU* 4.0 31.0 - - + -
223A VAL* 3.9 22.9 - - + -
226A ILE* 4.3 12.8 - - + -
243A MET* 4.6 2.2 - - + -
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Residues in contact with ILE 127 (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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43A VAL* 3.4 8.5 - - + +
45A CYS* 4.2 17.7 - - - -
125A VAL* 4.1 11.4 - - + +
126A PHE* 1.3 76.2 - - - +
128A THR* 1.3 63.7 + - - +
129A CYS* 5.8 0.4 - - - -
140A ALA* 4.0 21.8 - - + +
143A VAL* 3.9 15.9 - - + +
144A ALA* 3.3 46.9 - - + +
154A THR* 4.0 12.3 - - + -
155A VAL 2.7 13.6 + - - +
156A ALA* 3.1 11.5 - - + +
157A VAL* 2.8 27.2 + - - +
158A VAL* 4.3 2.2 - - + +
180A LEU* 5.1 2.0 - - + -
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Residues in contact with THR 128 (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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42A VAL* 4.4 14.6 - - + -
43A VAL 2.8 19.4 + - - +
44A GLY* 3.3 11.4 - - - -
45A CYS* 3.1 19.9 + - - +
49A GLY* 3.8 1.4 - - - +
52A THR* 4.3 26.1 + - + +
53A ILE* 4.9 1.1 - - + -
126A PHE* 5.5 0.9 - - - -
127A ILE* 1.3 76.2 - - - +
129A CYS* 1.3 68.1 + - - +
157A VAL* 2.9 19.0 + - - -
158A VAL* 4.8 0.2 - - - -
215A LEU* 3.7 17.2 - - - +
219A VAL* 4.0 14.5 - - + +
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Residues in contact with CYS 129 (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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45A CYS* 3.2 26.5 - - + +
48A ALA* 4.7 2.2 - - - -
49A GLY* 4.0 8.5 - - - -
127A ILE* 5.8 0.2 - - - -
128A THR* 1.3 82.3 + - - +
130A GLY* 1.3 61.3 + - - +
131A LEU* 3.7 27.6 - - - -
136A GLY* 3.9 22.2 - - - -
140A ALA* 4.1 9.6 - - - -
157A VAL 3.7 1.8 + - - +
158A VAL* 3.3 33.2 - - - +
159A THR* 3.4 4.2 + - - +
215A LEU* 5.0 6.0 - - - +
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Residues in contact with GLY 130 (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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45A CYS 4.8 0.4 + - - -
48A ALA* 3.8 15.2 - - - +
129A CYS* 1.3 80.7 - - - +
131A LEU* 1.3 62.8 + - - -
132A GLY 3.7 0.5 + - - -
133A GLY 4.3 1.0 + - - -
137A THR* 4.4 3.3 + - - -
159A THR* 3.4 17.3 - - - -
215A LEU* 5.7 0.7 - - - -
500A GTP 3.2 41.2 + - - +
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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