Contacts of the strand formed by residues 132 - 139 (chain B) in PDB entry 2X1W
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 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127B ARG 5.0 2.0 - - - +
128B LYS* 4.1 11.7 - - - +
130B GLN* 3.5 26.5 - - + +
131B CYS* 1.3 78.0 - - - +
133B PRO* 1.3 83.9 - - + +
134B ARG* 3.5 36.7 + - + +
163B GLY 3.0 28.6 + - - +
209B CYS* 3.4 12.1 - - - +
2H NAG 6.5 0.7 - - - -
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Residues in contact with PRO 133 (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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132B MET* 1.3 98.6 - - + +
134B ARG* 1.3 62.6 + - - +
160B TYR* 3.9 19.4 - - + -
161B ARG 3.6 7.6 - - - +
206B HIS 3.7 17.3 - - - +
207B THR 4.0 25.4 - - - +
208B SER* 4.2 0.7 - - - +
209B CYS* 3.3 21.0 - - + +
1H NAG 4.3 8.7 - - - +
2H NAG 4.5 13.7 - - + +
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Residues in contact with ARG 134 (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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135A GLU* 4.8 13.9 + - - +
136A VAL* 4.9 2.0 - - - +
137A ALA* 4.7 15.2 - - - +
128B LYS 3.1 26.9 + - - -
129B THR* 3.5 10.5 + - - +
130B GLN 2.9 22.8 + - - -
132B MET* 3.6 22.9 + - + +
133B PRO* 1.3 78.4 - - - +
135B GLU* 1.3 65.7 + - - +
136B VAL* 3.3 9.0 + - + +
160B TYR* 3.5 8.5 - - - -
161B ARG* 2.7 37.1 + - - +
163B GLY* 2.8 35.4 + - - -
164B GLY* 3.9 6.7 - - - +
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Residues in contact with GLU 135 (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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128A LYS* 4.2 23.6 + - - +
134A ARG* 4.8 11.5 + - - +
134B ARG* 1.3 73.8 - - - +
136B VAL* 1.3 64.0 + - - +
158B SER* 3.7 22.9 + - - +
159B VAL 3.4 4.9 - - - +
160B TYR* 3.4 44.8 + - + -
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Residues in contact with VAL 136 (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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134A ARG* 4.9 6.1 - - - +
134B ARG* 3.9 11.9 - - + +
135B GLU* 1.3 80.5 - - - +
137B ALA* 1.3 61.6 + - - +
138B ILE* 3.7 17.7 + - + -
157B VAL 3.6 0.3 - - - +
158B SER* 3.6 7.6 + - - -
159B VAL 2.8 39.0 + - - +
161B ARG* 3.7 33.9 - - + +
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Residues in contact with ALA 137 (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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128A LYS 5.4 0.2 - - - +
129A THR* 4.0 23.3 - - + -
134A ARG* 4.7 7.6 - - - +
164A GLY* 4.2 16.4 - - - +
165A CYS* 3.9 23.9 - - - -
136B VAL* 1.3 75.6 - - - +
138B ILE* 1.3 63.7 + - - +
139B ASP 3.9 1.9 + - - -
156B CYS* 4.5 0.4 - - - -
157B VAL 3.6 5.4 - - - -
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Residues in contact with ILE 138 (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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136B VAL* 3.8 17.7 - - + -
137B ALA* 1.3 75.0 - - - +
139B ASP* 1.3 72.4 + - - +
140B VAL 3.3 1.5 + - - +
143B GLU* 3.4 32.1 - - + +
156B CYS* 3.0 6.6 - - - -
157B VAL* 3.0 44.4 + - + +
159B VAL* 3.5 27.1 - - + -
161B ARG* 3.6 22.2 - - + +
203B PHE* 4.8 4.9 - - + -
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Residues in contact with ASP 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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165A CYS* 5.3 0.4 - - - -
137B ALA 3.9 2.8 + - - -
138B ILE* 1.3 71.9 - - - +
140B VAL* 1.3 62.9 + - - +
141B GLY* 3.1 7.2 + - - -
142B LYS* 2.8 49.1 + - + +
143B GLU* 3.1 21.3 + - - +
155B PRO* 4.3 10.2 - - - +
156B CYS* 3.6 17.7 - - - -
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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