Contacts of the strand formed by residues 138 - 145 (chain B) in PDB entry 4WGK
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 TYR 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 3.7 26.7 - - + -
109B ALA 3.3 14.1 - - - +
110B ASP* 4.1 12.8 - - + -
111B CYS* 3.5 5.2 - - - -
135B THR* 5.1 2.7 - - - -
136B ARG* 3.5 29.8 - - + +
137B LEU* 1.3 77.4 - - - +
139B SER* 1.3 61.8 + - - +
140B ARG* 3.6 27.9 + - - +
157B SER 3.9 1.7 - - - +
158B ILE* 3.7 1.0 - - - -
159B ASP* 2.7 46.9 + - - +
316B SER* 6.1 0.2 - - - -
324B TYR* 6.3 3.1 - + - -
327B GLU* 5.4 0.9 - - - -
336B PRO* 4.1 0.3 + - - +
337B GLY* 3.2 37.2 + - - -
713B ALA* 3.3 26.0 - - + +
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Residues in contact with SER 139 (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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108B ARG* 3.3 2.3 - - - -
109B ALA 2.8 32.9 + - - -
111B CYS* 3.6 8.3 - - - -
138B TYR* 1.3 73.0 - - - +
140B ARG* 1.3 58.3 + - - +
156B VAL* 3.3 19.8 - - - +
157B SER 3.8 3.1 - - - -
158B ILE* 4.3 4.0 - - - +
226B GLY 3.7 8.3 - - - -
227B ILE* 3.3 29.9 - - - +
230B SER* 3.0 23.8 + - - -
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Residues in contact with ARG 140 (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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107B GLY 3.3 3.4 - - - -
108B ARG* 3.8 10.6 - - + +
138B TYR* 3.6 27.8 + - + +
139B SER* 1.3 79.7 + - - +
141B ALA* 1.3 58.3 + - - +
142B PHE* 3.7 8.0 - - + -
156B VAL* 3.3 3.2 - - - -
157B SER 2.9 43.9 + - - +
159B ASP* 3.4 29.5 + - - -
320B GLY* 5.5 1.8 + - - -
323B SER* 4.1 20.5 + - - -
324B TYR* 5.0 2.2 - - - +
327B GLU* 2.8 39.6 + - - -
342B VAL* 3.6 20.9 - - + -
343B ALA 3.3 19.8 + - - -
344B ALA* 3.6 21.9 - - + +
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Residues in contact with ALA 141 (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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106B VAL* 3.4 4.3 - - - -
107B GLY 2.9 31.2 + - - +
139B SER 4.1 0.4 - - - -
140B ARG* 1.3 72.1 - - - +
142B PHE* 1.3 68.8 + - - +
143B ILE* 4.3 0.7 - - + -
154B VAL* 4.7 2.9 - - + -
155B PHE 3.5 4.3 - - - -
156B VAL* 3.9 9.6 - - + -
230B SER* 3.8 34.1 - - - +
231B ILE* 3.8 18.8 - - + +
234B ALA* 4.5 4.5 - - + -
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Residues in contact with PHE 142 (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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105B GLY 3.5 3.4 - - - +
106B VAL* 3.6 20.6 - - + -
140B ARG 3.7 14.6 - - - -
141B ALA* 1.3 73.3 - - - +
143B ILE* 1.3 63.5 + - - +
144B MET* 3.6 16.4 - - + +
153B THR 3.5 1.7 - - - +
154B VAL* 3.4 4.8 - - - +
155B PHE* 2.8 46.9 + + + +
286B MET* 3.5 30.7 - - + -
296B LEU 3.5 20.0 - - - -
297B ILE* 3.8 24.9 - - + -
342B VAL* 3.8 27.1 - - + -
344B ALA* 3.6 25.6 - - + -
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Residues in contact with ILE 143 (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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103B HIS 3.5 0.9 - - - +
104B ILE* 3.3 5.4 - - - -
105B GLY* 2.8 42.5 + - - +
141B ALA* 5.2 0.9 - - + -
142B PHE* 1.3 77.1 - - - +
144B MET* 1.3 71.6 + - - +
152B ARG* 4.5 3.6 - - + -
153B THR 3.4 8.1 - - - +
154B VAL* 4.1 12.6 - - + -
183B TYR* 3.6 42.2 - - + +
231B ILE* 3.8 19.5 - - + +
234B ALA* 3.8 9.9 - - + -
235B HIS* 3.7 24.0 - - - +
238B MET* 3.9 18.7 - - + +
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Residues in contact with MET 144 (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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102B TYR* 5.0 3.8 - - + -
103B HIS 3.4 3.6 - - - -
104B ILE* 4.5 9.6 - - + -
142B PHE* 3.6 26.7 - - + +
143B ILE* 1.3 86.3 - - - +
145B ALA* 1.3 60.9 + - - +
152B ARG* 3.2 5.4 - - - +
153B THR* 2.9 49.9 + - - +
155B PHE* 5.0 8.1 - - + +
243B ILE* 3.7 27.6 - - + -
284B LEU* 6.0 0.7 - - - -
286B MET* 4.5 15.9 - - - +
297B ILE* 5.8 2.7 - - + -
423B LEU* 3.6 13.9 - - + +
529B LEU* 3.6 27.8 - - + -
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Residues in contact with ALA 145 (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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102B TYR* 3.4 10.2 - - - +
103B HIS* 2.9 32.0 + - + +
144B MET* 1.3 76.2 - - - +
146B GLU* 1.3 66.6 + - - +
149B GLY* 4.2 6.3 - - - +
150B SER 4.0 3.6 - - - +
152B ARG* 3.8 27.1 - - + +
238B MET* 3.8 19.3 - - + -
423B LEU* 3.6 9.6 - - - -
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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