Contacts of the strand formed by residues 256 - 263 (chain A) in PDB entry 1ML3
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 SER 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A THR* 4.1 0.4 - - - -
193A ILE 3.2 15.9 - - - -
194A HIS* 3.3 12.7 + - - -
195A SER 3.2 21.0 + - - -
255A VAL* 1.3 73.0 - - - +
257A VAL* 1.3 65.1 + - - +
332A TRP* 3.5 12.0 - - - -
333A TYR* 3.0 55.3 + - - +
335A ASN* 3.3 9.5 + - - -
221B ILE* 4.5 1.8 - - - -
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Residues in contact with VAL 257 (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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191A THR 3.9 0.3 - - - +
192A THR* 3.2 7.3 + - - -
193A ILE* 3.1 48.5 + - + +
256A SER* 1.3 80.2 - - - +
258A VAL* 1.3 63.4 + - - +
330A VAL* 3.4 30.1 - - + -
331A SER 3.3 16.8 - - - +
332A TRP* 3.8 20.6 - - + -
333A TYR* 3.8 6.1 - - - -
221B ILE* 4.5 6.5 - - + -
248B PHE* 4.0 20.0 - - + -
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Residues in contact with VAL 258 (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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167A THR* 4.6 11.9 - - + -
170A CYS* 3.2 31.9 - - + -
171A LEU* 4.4 22.9 - - + +
174A ILE* 5.9 2.5 - - + -
190A MET* 4.7 10.8 - - - -
191A THR 3.9 2.0 - - - -
192A THR* 4.9 1.1 - - - -
257A VAL* 1.3 74.1 - - - +
259A ASP* 1.3 63.2 + - - +
260A LEU* 3.9 21.1 - - + +
329A ILE 3.3 2.2 - - - +
330A VAL* 3.1 10.4 - - - +
331A SER* 2.6 46.4 + - - +
333A TYR* 3.8 12.6 - - + +
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Residues in contact with ASP 259 (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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189A LEU 3.9 0.5 - - - +
190A MET* 3.4 1.7 - - - -
191A THR* 2.7 47.5 + - - +
193A ILE* 4.6 10.1 - - + -
257A VAL 3.9 0.4 + - - -
258A VAL* 1.3 73.6 - - - +
260A LEU* 1.3 57.6 + - - +
261A THR* 3.8 3.8 + - - -
328A LYS* 2.5 36.2 + - - +
329A ILE 3.8 2.0 - - - -
330A VAL* 4.6 2.3 - - - +
191B THR* 2.5 39.8 + - - +
248B PHE* 3.8 12.2 - - + -
259B ASP* 4.9 0.3 - - - +
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Residues in contact with LEU 260 (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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171A LEU* 3.8 25.6 - - + -
174A ILE* 4.2 19.5 - - + -
175A VAL* 4.3 9.2 - - + -
178A LEU* 4.5 5.4 - - + -
185A VAL* 6.3 0.7 - - + -
188A GLY* 4.8 3.6 - - - -
189A LEU 3.6 15.7 - - - +
190A MET* 4.1 13.0 - - + +
243A LEU* 5.3 6.7 - - + -
258A VAL* 4.2 12.3 - - + -
259A ASP* 1.3 73.2 - - - +
261A THR* 1.3 74.1 + - - +
262A PHE* 4.2 25.6 - - + -
327A PHE 3.7 0.9 - - - +
328A LYS* 3.2 4.5 - - - -
329A ILE* 2.8 48.3 + - + +
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Residues in contact with THR 261 (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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188A GLY* 3.3 1.0 - - - -
189A LEU 2.7 45.6 + - - -
259A ASP* 3.8 3.1 + - - -
260A LEU* 1.3 74.1 + - - +
262A PHE* 1.3 62.6 + - - +
326A PHE* 4.0 18.8 - - + -
327A PHE 3.3 10.8 - - - +
328A LYS* 3.6 22.2 + - - +
189B LEU* 4.3 7.0 - - + +
261B THR* 3.4 39.2 + - + -
326B PHE* 3.3 7.4 - - + -
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Residues in contact with PHE 262 (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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178A LEU* 3.8 20.4 - - + -
183A PHE* 5.5 0.9 - - + -
184A GLY 4.1 8.7 - - - -
185A VAL* 4.5 14.1 - - + -
187A THR 3.3 15.3 - - - +
188A GLY* 3.9 5.2 - - - -
260A LEU* 4.2 23.1 - - + -
261A THR* 1.3 76.9 - - - +
263A THR* 1.3 74.6 + - - +
264A ALA* 3.7 25.6 - - + -
273A ILE* 3.9 23.1 - - + -
325A ARG 3.2 1.2 - - - +
326A PHE* 3.6 1.7 - - - -
327A PHE* 2.8 54.6 + + + -
329A ILE* 3.4 24.5 - - + -
326B PHE* 3.9 4.9 - - - -
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Residues in contact with THR 263 (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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186A GLN* 2.9 48.0 + - - +
187A THR* 3.1 14.6 + - - -
262A PHE* 1.3 76.3 - - - +
264A ALA* 1.3 64.7 + - - +
325A ARG* 3.0 13.7 - - + +
326A PHE* 3.6 20.0 - - + -
263B THR* 4.6 5.8 - - + -
326B PHE* 3.4 29.2 - - + -
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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