Contacts of the strand formed by residues 256 - 263 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE* 4.7 1.8 - - - -
192B THR* 4.3 0.2 - - - -
193B ILE 3.4 14.6 - - - -
194B HIS* 3.5 14.1 + - - -
195B SER 3.4 14.2 + - - -
255B VAL* 1.3 71.8 - - - +
257B VAL* 1.3 65.0 + - - +
332B TRP* 3.5 8.6 - - - -
333B TYR* 2.8 58.4 + - - +
335B ASN* 3.0 16.0 + - - -
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE* 4.4 5.2 - - + -
248A PHE* 4.2 12.8 - - + -
192B THR* 3.3 2.9 - - - -
193B ILE* 2.9 58.0 + - + +
256B SER* 1.3 79.5 - - - +
258B VAL* 1.3 64.5 + - - +
259B ASP 3.9 0.2 + - - -
330B VAL* 3.7 24.9 - - + -
331B SER 3.3 24.0 - - - +
332B TRP* 3.6 29.4 - - + -
333B TYR* 4.0 2.9 - - - -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B THR* 4.2 7.9 - - + +
170B CYS* 3.6 27.6 - - + -
171B LEU* 4.4 18.4 - - + +
174B ILE* 6.0 2.0 - - + -
190B MET* 4.1 23.6 - - + -
191B THR 3.7 2.9 - - - +
192B THR* 4.4 3.8 - - - +
257B VAL* 1.3 75.7 - - - +
259B ASP* 1.3 63.2 + - - +
260B LEU* 4.0 20.6 - - + +
329B ILE 3.7 1.2 - - - +
330B VAL* 3.5 5.5 - - - +
331B SER* 2.7 42.9 + - - +
333B TYR* 3.9 11.4 - - + -
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Residues in contact with ASP 259 (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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191A THR* 2.7 37.5 + - - +
248A PHE* 4.2 11.0 - - + -
259A ASP* 4.9 0.5 - - - +
189B LEU 4.0 0.5 - - - +
190B MET* 3.6 1.4 - - - -
191B THR* 2.6 48.0 + - - +
193B ILE* 4.2 13.9 - - + -
258B VAL* 1.3 73.4 - - - +
260B LEU* 1.3 59.0 + - - +
261B THR* 4.0 3.4 + - - -
328B LYS* 3.0 34.5 + - - +
329B ILE 3.9 1.8 - - - -
330B VAL* 4.3 4.1 - - - +
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Residues in contact with LEU 260 (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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171B LEU* 3.9 28.3 - - + -
174B ILE* 4.1 21.1 - - + -
175B VAL* 4.5 5.4 - - + -
178B LEU* 4.3 10.1 - - + -
185B VAL* 6.3 0.4 - - + -
188B GLY* 4.8 4.0 - - - -
189B LEU 3.6 19.1 - - - +
190B MET* 4.2 6.7 - - + +
243B LEU* 5.6 4.9 - - + -
258B VAL* 3.8 13.0 - - + -
259B ASP* 1.3 73.2 + - - +
261B THR* 1.3 69.5 - - - +
262B PHE* 4.2 25.0 - - + -
327B PHE 3.9 0.5 - - - +
328B LYS* 3.2 4.2 - - - +
329B ILE* 2.7 46.4 + - + +
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Residues in contact with THR 261 (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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189A LEU* 4.3 5.1 + - + +
261A THR* 3.4 38.5 + - + -
326A PHE* 3.2 5.9 - - + -
188B GLY* 3.4 0.2 - - - -
189B LEU 2.9 36.9 + - - -
259B ASP* 4.0 3.9 + - - -
260B LEU* 1.3 76.0 + - - +
262B PHE* 1.3 63.5 + - - +
326B PHE* 3.8 22.9 - - + -
327B PHE 3.2 10.8 - - - +
328B LYS* 3.8 22.9 + - - +
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Residues in contact with PHE 262 (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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326A PHE* 3.8 6.3 - - - -
178B LEU* 3.6 37.0 - - + -
183B PHE* 5.4 0.7 - - + -
184B GLY 3.9 16.8 - - - -
185B VAL* 4.3 11.0 - - + -
187B THR 3.1 15.7 - - - +
188B GLY* 4.0 5.2 - - - -
260B LEU* 4.2 20.0 - - + -
261B THR* 1.3 77.4 - - - +
263B THR* 1.3 72.6 + - - +
264B ALA* 4.0 14.6 - - + -
273B ILE* 4.2 13.0 - - + -
325B ARG 3.3 0.9 - - - +
326B PHE* 3.4 3.1 - - - -
327B PHE* 2.8 58.9 + + + -
329B ILE* 3.6 25.6 - - + -
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Residues in contact with THR 263 (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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263A THR* 4.6 5.6 - - + -
326A PHE* 3.9 11.2 - - + -
186B GLN* 2.9 37.4 + - - +
187B THR* 2.8 28.6 + - - +
262B PHE* 1.3 80.5 - - - +
264B ALA* 1.3 65.0 + - - +
325B ARG* 3.0 13.9 - - + +
326B PHE* 3.8 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