Contacts of the helix formed by residues 256 - 267 (chain B) in PDB entry 1H4L
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 ASN 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104B LYS* 5.5 6.3 - - - +
255B LEU* 1.3 68.7 - - - +
257B ALA* 1.3 57.1 + - - +
258B THR* 3.2 18.8 - - + +
259B GLY* 3.0 26.5 + - - -
260B ARG* 2.8 42.7 + - - +
285B TYR* 4.0 12.5 - - - -
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Residues in contact with ALA 257 (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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256B ASN* 1.3 74.4 - - - +
258B THR* 1.3 62.2 + - - +
260B ARG* 2.9 30.3 + - - +
261B ASP* 3.3 20.3 + - - +
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Residues in contact with THR 258 (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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256B ASN* 3.2 26.7 - - + +
257B ALA* 1.3 73.0 - - - +
259B GLY* 1.3 72.4 + - - +
261B ASP* 3.0 17.5 + - - +
262B LEU 3.3 8.3 + - - -
283B HIS* 3.4 6.7 - - - -
284B PRO* 3.8 12.2 - - - +
285B TYR* 3.1 33.6 + - + +
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Residues in contact with GLY 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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192B PHE* 3.5 9.1 - - - -
255B LEU* 4.0 9.0 - - - -
256B ASN* 3.0 16.1 + - - -
258B THR* 1.3 78.8 - - - +
260B ARG* 1.3 57.1 + - - +
262B LEU* 3.3 4.7 + - - +
263B LEU 3.0 22.5 + - - -
285B TYR* 3.2 33.7 - - - -
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Residues in contact with ARG 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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248B LEU* 4.6 5.0 - - + +
249B VAL* 2.8 53.5 - - - +
252B VAL* 4.3 10.8 - - + -
255B LEU* 3.5 33.3 + - + +
256B ASN* 2.8 28.4 + - - +
257B ALA* 2.9 46.7 + - - +
259B GLY* 1.3 72.7 - - - +
261B ASP* 1.3 66.7 + - - +
263B LEU* 3.3 6.3 + - - +
264B GLN* 2.9 32.2 + - + +
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Residues in contact with ASP 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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257B ALA 3.3 11.3 + - - +
258B THR* 3.0 11.5 + - - +
260B ARG* 1.3 78.9 - - - +
262B LEU* 1.3 62.3 + - - +
264B GLN* 2.9 26.2 + - - +
265B ASN* 3.0 25.1 + - - -
283B HIS* 2.6 29.8 + - + +
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Residues in contact with LEU 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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107B LEU* 4.2 14.4 - - + -
111B LEU* 4.7 4.5 - - + -
192B PHE* 4.5 1.3 - - + -
258B THR 3.3 2.9 + - - +
259B GLY* 3.3 12.2 + - - +
261B ASP* 1.3 78.5 + - - +
263B LEU* 1.3 55.8 + - - +
265B ASN* 2.7 25.9 + - + +
266B LEU* 3.1 19.8 + - + +
275B ILE* 3.9 34.5 - - + -
280B ALA* 4.3 12.6 - - + +
283B HIS* 3.8 25.8 - - + +
285B TYR* 4.1 27.1 - - + -
286B PHE* 4.2 15.5 - - + -
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Residues in contact with LEU 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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189B GLY* 3.6 27.8 - - - +
192B PHE* 3.9 21.7 - - + -
193B ALA* 4.2 16.8 - - + +
202B LEU* 5.5 0.4 - - + -
248B LEU* 3.4 24.9 - - + -
251B VAL* 5.4 2.2 - - + -
252B VAL* 3.9 25.6 - - + -
255B LEU* 4.6 3.8 - - + -
259B GLY 3.0 14.2 + - - +
260B ARG* 3.5 9.6 - - - +
261B ASP 3.3 0.2 - - - -
262B LEU* 1.3 75.7 - - - +
264B GLN* 1.3 61.0 + - - +
266B LEU* 3.3 4.3 + - - +
267B LEU* 3.1 36.9 + - + +
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Residues in contact with GLN 264 (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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246B THR* 3.0 31.7 + - - -
247B SER* 4.9 1.8 - - - +
248B LEU* 4.0 23.3 - - + +
260B ARG* 2.9 25.3 + - - +
261B ASP* 2.9 18.6 + - - +
263B LEU* 1.3 77.6 - - - +
265B ASN* 1.3 61.7 + - - +
266B LEU 3.4 0.5 + - - -
267B LEU* 3.5 9.1 + - - -
268B LYS* 3.5 26.2 + - - +
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Residues in contact with ASN 265 (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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261B ASP* 3.0 33.3 + - - +
262B LEU* 2.7 16.6 + - - +
264B GLN* 1.3 73.6 - - - +
266B LEU* 1.3 56.6 + - - +
268B LYS* 4.0 14.3 - - - +
273B GLN* 4.0 11.3 - - - +
274B ARG* 3.5 6.2 - - - -
275B ILE* 2.8 52.2 + - + +
283B HIS* 4.9 4.9 + - - -
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Residues in contact with LEU 266 (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 LEU* 5.1 6.1 - - + -
111B LEU* 4.8 5.8 - - + -
185B MET* 3.2 41.3 - - + +
186B TRP* 3.7 16.5 - - - -
188B ALA* 4.4 3.8 - - + -
189B GLY* 3.4 32.8 - - - +
192B PHE* 4.2 24.0 - - + -
262B LEU* 3.1 26.7 + - + +
263B LEU* 3.7 5.4 - - - +
265B ASN* 1.3 78.0 - - - +
267B LEU* 1.3 59.7 + - - +
268B LYS 3.3 6.2 + - - -
274B ARG* 3.6 15.8 - - - +
275B ILE* 3.6 15.3 - - + +
280B ALA* 4.9 1.8 - - + -
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Residues in contact with LEU 267 (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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186B TRP* 3.2 47.0 - - + +
189B GLY 4.1 1.8 - - - -
190B CYS* 3.8 16.8 - - - +
202B LEU* 3.7 29.6 - - + -
203B PHE* 4.2 7.4 - - + -
218B LEU* 5.5 0.2 - - + -
219B LEU* 2.9 40.2 - - + +
248B LEU* 4.9 6.1 - - + -
263B LEU* 3.1 37.8 + - + +
264B GLN* 3.5 7.4 + - - +
265B ASN 3.5 0.4 - - - -
266B LEU* 1.3 77.5 - - - +
268B LYS* 1.3 58.0 + - - -
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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