Contacts of the helix formed by residues 255 - 267 (chain B) in PDB entry 2H3W
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 HIS 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B ARG* 3.2 32.8 + - + +
112B GLN* 3.6 23.0 + - - -
113B PRO* 3.6 18.2 - - + +
254B ASN* 1.3 82.3 + - - +
256B ARG* 1.3 54.1 + - - +
257B ASN* 3.1 44.9 + - + +
258B THR* 3.0 18.9 + - - +
259B TRP* 2.6 32.7 + - - +
399B ASN* 5.5 2.5 - - - +
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Residues in contact with ARG 256 (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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110B PHE 3.7 9.4 - - - +
111B ARG* 2.9 47.2 + - - +
112B GLN 3.3 16.2 - - - +
114B VAL* 3.6 27.5 - - - +
181B ARG* 3.7 10.7 - - - +
183B PRO* 3.8 11.3 - - - +
188B ASP* 2.8 29.9 + - - +
252B THR 3.7 13.9 + - - -
254B ASN 3.4 6.8 + - - -
255B HIS* 1.3 67.5 - - - +
257B ASN* 1.3 57.6 + - - +
259B TRP* 3.3 28.2 - - - +
260B ALA* 2.7 35.7 + - - +
324B ASP* 2.8 31.5 + - - -
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Residues in contact with ASN 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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111B ARG* 2.7 43.6 + - - +
185B PRO 4.3 6.0 - - - +
255B HIS* 3.1 25.1 + - + -
256B ARG* 1.3 77.6 - - - +
258B THR* 1.3 64.6 + - - +
260B ALA* 3.4 8.0 + - - +
261B LYS* 3.4 13.7 + - - +
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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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254B ASN* 3.6 30.5 + - - +
255B HIS* 3.0 21.7 + - - +
257B ASN* 1.3 75.9 - - - +
259B TRP* 1.3 65.5 + - - +
261B LYS* 3.2 6.7 + - - +
262B ALA* 2.9 26.3 + - + +
392B ASP* 6.0 1.8 - - - +
395B LYS* 5.9 3.6 - - + -
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Residues in contact with TRP 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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183B PRO* 3.0 17.8 - - + +
251B LEU* 3.4 48.5 - - + +
252B THR* 3.5 28.0 - - + +
254B ASN* 4.2 6.7 - - - +
255B HIS 2.6 19.7 + - - +
256B ARG* 3.3 33.0 - - - +
258B THR* 1.3 74.1 - - - +
260B ALA* 1.3 53.6 + - - +
262B ALA* 4.0 8.7 - - + -
263B TYR* 2.7 74.3 + + - +
266B LEU* 4.1 13.2 - - + -
322B TRP* 4.1 8.5 - + - -
324B ASP* 2.6 26.1 + - - -
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ARG* 4.1 1.1 - - - +
183B PRO* 3.8 14.3 - - + +
184B GLY* 3.4 34.5 - - - +
185B PRO* 3.9 11.6 - - + +
256B ARG 2.7 23.0 + - - +
257B ASN 3.5 6.3 - - - +
258B THR 3.2 0.2 - - - -
259B TRP* 1.3 74.1 - - - +
261B LYS* 1.3 56.8 + - - +
263B TYR* 3.7 3.6 - - - +
264B ASN* 3.1 26.9 + - - +
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Residues in contact with LYS 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 ASN 3.4 7.5 + - - +
258B THR* 3.2 8.4 + - - +
259B TRP 3.2 0.4 - - - -
260B ALA* 1.3 77.5 - - - +
262B ALA* 1.3 66.3 + - - +
264B ASN* 3.4 5.9 + - - +
265B ASN* 3.2 22.3 + - + +
388B GLU* 6.0 1.8 - - - -
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Residues in contact with ALA 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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251B LEU* 4.6 8.4 - - + +
258B THR* 2.9 19.8 + - + +
259B TRP* 3.9 17.9 - - + +
261B LYS* 1.3 75.2 - - - +
263B TYR* 1.3 60.5 + - - +
265B ASN* 3.5 3.8 + - - +
266B LEU* 2.9 28.8 + - - +
389B ILE* 6.0 0.3 - - - +
392B ASP* 3.8 37.5 - - + +
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Residues in contact with TYR 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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182B VAL* 4.1 18.6 - - + +
183B PRO* 3.9 26.5 - - + -
259B TRP* 2.7 59.9 + + + +
260B ALA 3.7 4.3 - - - +
262B ALA* 1.3 71.8 - - - +
264B ASN* 1.3 69.9 + - + +
266B LEU* 3.0 15.9 + - + +
267B ILE* 3.0 47.2 + - + +
276B VAL* 3.8 24.6 - - + +
280B GLN* 3.2 29.6 + - - -
322B TRP* 5.0 2.9 - + - -
324B ASP* 5.6 0.2 - - - -
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Residues in contact with ASN 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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260B ALA 3.1 15.3 + - - +
261B LYS* 3.6 7.4 - - + +
263B TYR* 1.3 85.4 - - + +
265B ASN* 1.3 62.6 + - - +
267B ILE* 3.4 23.3 - - - +
268B LYS* 3.5 27.2 + - - +
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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 LYS* 3.2 14.1 + - + +
262B ALA* 3.8 5.6 + - - +
264B ASN* 1.3 77.0 + - - +
266B LEU* 1.3 67.4 + - - +
268B LYS* 3.1 49.7 + - - +
269B ASP 4.5 0.2 + - - -
386B THR* 4.6 1.0 + - - -
388B GLU* 2.6 46.8 + - - +
389B ILE* 3.6 24.4 - - - +
392B ASP* 4.3 6.1 + - - +
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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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248B VAL* 4.1 29.6 - - + -
251B LEU* 4.3 6.1 - - + -
259B TRP* 4.1 22.7 - - + -
262B ALA 2.9 15.2 + - - +
263B TYR* 3.0 10.5 + - + +
265B ASN* 1.3 78.9 - - - +
267B ILE* 1.3 56.6 + - - +
268B LYS 3.2 4.9 + - - -
269B ASP* 3.7 2.3 + - - +
272B ASN* 3.0 50.9 + - + +
276B VAL* 4.1 23.3 - - + -
322B TRP* 4.4 1.6 - - + -
383B PHE* 4.3 4.5 - - + -
385B ILE* 5.4 0.9 - - + -
389B ILE* 4.0 32.3 - - + +
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Residues in contact with ILE 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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263B TYR* 3.0 58.9 + - + +
264B ASN* 3.4 17.7 - - - +
266B LEU* 1.3 74.1 - - + +
268B LYS* 1.3 53.9 + - - +
269B ASP 3.3 5.4 - - - -
273B ARG* 2.7 53.8 + - + +
276B VAL* 4.0 25.4 - - + -
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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