Contacts of the strand formed by residues 124 - 132 (chain B) in PDB entry 2W5X
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 LYS 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ASN* 3.9 15.2 + - - -
123B ILE* 1.3 73.0 - - - +
125B THR* 1.3 58.5 + - - +
164B ASP* 3.4 24.1 + - + -
209B ARG* 3.6 33.2 - - - +
241B PHE* 6.0 2.2 - - + -
242B LEU* 3.6 35.9 - - + +
247B SER* 3.3 21.9 + - - +
248B ALA 3.0 9.9 + - - +
249B PHE* 3.1 5.7 - - - +
250B PHE 2.8 27.0 + - - +
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Residues in contact with THR 125 (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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115B VAL* 3.7 28.6 - - + +
118B ALA* 3.4 32.5 - - + -
119B ALA* 4.5 2.0 - - + +
123B ILE 3.7 5.6 - - - +
124B LYS* 1.3 78.7 - - - +
126B GLY* 1.3 59.5 + - - +
162B ASP 3.4 8.5 + - - +
163B LEU* 3.3 25.9 - - - +
164B ASP* 2.9 36.9 + - - +
165B PHE 3.1 5.7 + - - -
242B LEU* 3.6 4.7 - - - +
250B PHE* 3.3 11.4 - - + +
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Residues in contact with GLY 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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115B VAL* 6.0 0.2 - - - +
125B THR* 1.3 76.1 - - - +
127B VAL* 1.3 68.8 + - - +
128B VAL* 5.5 0.2 - - - -
163B LEU* 4.1 0.4 - - - -
165B PHE* 3.2 15.7 - - - -
242B LEU* 3.5 15.8 - - - +
250B PHE* 2.9 11.2 + - - +
251B ILE* 3.3 7.7 - - - -
252B MET 3.0 24.0 + - - -
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Residues in contact with VAL 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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115B VAL* 5.1 3.4 - - + -
126B GLY* 1.3 80.1 - - - +
128B VAL* 1.3 67.0 + - - +
133B ILE* 4.0 9.0 - - + +
138B PRO* 3.7 32.5 - - + +
141B PHE* 4.2 22.2 - - + -
142B TYR* 4.9 2.0 - - + -
163B LEU* 3.8 30.5 - - + -
165B PHE* 3.1 7.9 + - - -
166B PHE* 3.0 8.7 - - + +
167B ALA 3.0 23.2 + - - +
250B PHE* 5.9 0.2 - - + -
252B MET* 3.3 22.4 - - + +
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Residues in contact with VAL 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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127B VAL* 1.3 81.7 - - - +
129B ALA* 1.3 65.6 + - - +
133B ILE* 4.8 0.2 - - - -
165B PHE* 4.1 22.9 - - + -
167B ALA* 3.3 10.1 - - + +
230B PHE* 4.3 5.8 - - + -
231B LEU* 4.0 21.8 - - + -
234B ALA* 3.8 33.9 - - + +
235B THR* 4.5 1.8 - - - +
238B ALA* 4.6 6.5 - - + -
251B ILE* 5.1 2.0 - - + -
252B MET* 2.8 11.2 + - - +
253B SER* 3.4 21.2 - - - +
254B GLU* 2.8 23.8 + - - +
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Residues in contact with ALA 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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128B VAL* 1.3 76.9 - - - +
130B THR* 1.3 64.0 + - - +
131B SER* 3.4 9.4 - - - +
132B SER 4.7 0.2 - - - +
133B ILE* 4.7 5.6 - - + -
138B PRO* 3.6 22.7 - - + -
167B ALA 3.0 6.9 + - - -
168B GLY* 3.3 15.2 - - - -
220B MET* 4.3 0.2 - - - +
230B PHE* 3.2 17.6 - - - -
254B GLU* 3.6 19.3 - - + +
256B SER* 3.5 11.9 - - - +
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Residues in contact with THR 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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129B ALA* 1.3 73.5 - - - +
131B SER* 1.3 59.7 + - - +
220B MET* 3.2 21.6 + - - +
227B ARG* 3.6 42.3 + - - +
230B PHE* 3.9 14.4 - - + -
231B LEU* 4.2 15.0 - - + -
254B GLU 3.6 8.9 + - - +
255B GLY* 4.1 1.0 - - - -
256B SER* 3.0 27.5 + - - +
257B GLN* 2.9 30.6 + - - +
273B GLU* 4.9 0.3 + - - -
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Residues in contact with SER 131 (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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129B ALA* 3.8 8.8 - - - +
130B THR* 1.3 81.6 - - - +
132B SER* 1.3 75.7 + - - +
135B GLU* 3.4 21.6 + - - +
138B PRO* 4.2 0.5 - - - +
168B GLY* 4.1 0.3 - - - -
169B GLY 3.0 18.4 + - - -
219B ALA* 4.2 5.8 - - - +
254B GLU* 3.8 6.6 + - - -
256B SER* 3.2 23.4 + - - -
260B TRP* 3.9 24.9 - - - -
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Residues in contact with SER 132 (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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131B SER* 1.3 89.5 + - - +
133B ILE* 1.3 64.7 + - - +
134B THR* 2.8 28.1 + - - +
135B GLU* 3.2 15.6 + - - +
138B PRO* 3.9 2.4 - - - +
151B GLU* 4.5 2.7 - - - -
169B GLY 3.5 10.8 - - - -
170B GLY* 3.2 22.7 - - - -
173B TYR* 3.6 11.3 - - - -
218B GLU* 3.9 8.7 - - - -
219B ALA* 4.0 7.9 - - - +
260B TRP* 5.3 0.4 - - - -
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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