Contacts of the helix formed by residues 255 - 267 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.0 31.2 + - + +
112A GLN* 3.8 23.3 + - - -
113A PRO* 3.7 16.5 - - + +
254A ASN* 1.3 85.5 + - - +
256A ARG* 1.3 59.3 + - - +
257A ASN* 3.0 55.4 + - + -
258A THR* 3.7 14.8 - - - +
259A TRP* 2.7 26.7 + - - +
399A ASN* 4.3 1.7 - - - +
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Residues in contact with ARG 256 (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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110A PHE 3.8 9.6 - - - +
111A ARG* 3.0 46.5 + - - +
112A GLN 3.4 16.2 - - - +
114A VAL* 3.7 29.4 - - - +
181A ARG* 3.7 11.6 - - - +
183A PRO* 4.1 7.1 - - - +
188A ASP* 2.7 31.5 + - - +
252A THR 3.7 14.5 + - - -
254A ASN 4.3 2.3 + - - -
255A HIS* 1.3 72.5 - - - +
257A ASN* 1.3 58.0 + - - +
259A TRP* 3.4 26.7 - - - +
260A ALA* 2.7 32.4 + - - +
324A ASP* 2.7 34.9 + - - -
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Residues in contact with ASN 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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111A ARG* 2.7 40.8 + - - +
185A PRO* 3.2 13.8 - - - +
186A LYS 4.7 0.2 - - - +
255A HIS* 3.0 30.7 + - + -
256A ARG* 1.3 77.3 - - - +
258A THR* 1.3 64.2 + - - +
260A ALA* 3.4 3.6 + - - +
261A LYS* 3.3 20.8 + - - +
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Residues in contact with THR 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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254A ASN* 3.7 28.7 + - - +
255A HIS* 3.2 21.0 + - - +
257A ASN* 1.3 76.8 - - - +
259A TRP* 1.3 59.9 + - - +
261A LYS* 3.3 7.0 + - - +
262A ALA* 2.9 29.9 + - + +
392A ASP* 5.8 3.1 - - - +
395A LYS* 5.9 3.6 - - + -
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Residues in contact with TRP 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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183A PRO* 3.0 18.0 - - + +
251A LEU* 3.4 48.5 - - + +
252A THR* 3.5 26.6 - - + +
254A ASN* 4.3 6.9 - - + +
255A HIS 2.7 23.2 + - - +
256A ARG* 3.4 29.8 - - - +
258A THR* 1.3 70.4 - - - +
260A ALA* 1.3 56.3 + - - +
262A ALA* 3.9 9.0 - - + -
263A TYR* 2.7 76.4 + + - +
266A LEU* 4.1 13.7 - - + -
322A TRP* 4.0 9.2 - + - -
324A ASP* 2.6 24.7 + - - -
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Residues in contact with ALA 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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183A PRO* 3.5 13.5 - - - +
184A GLY* 3.3 36.8 - - - +
185A PRO* 3.8 10.1 - - + -
256A ARG 2.7 22.8 + - - +
257A ASN 3.5 6.5 - - - +
259A TRP* 1.3 73.9 - - - +
261A LYS* 1.3 56.8 + - - +
263A TYR* 3.6 4.3 - - - +
264A ASN* 3.1 26.5 + - - +
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Residues in contact with LYS 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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257A ASN 3.3 8.3 + - - +
258A THR* 3.3 9.3 + - + +
259A TRP 3.2 0.4 - - - -
260A ALA* 1.3 77.8 - - - +
262A ALA* 1.3 65.3 + - - +
263A TYR 3.1 0.2 - - - -
264A ASN* 3.3 7.7 + - + +
265A ASN* 3.2 20.9 + - + +
388A GLU* 5.9 3.1 - - - -
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Residues in contact with ALA 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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251A LEU* 4.6 7.1 - - + +
258A THR* 2.9 20.8 + - + +
259A TRP* 3.9 17.5 - - + +
261A LYS* 1.3 76.5 - - - +
263A TYR* 1.3 57.7 + - - +
265A ASN* 3.3 4.6 + - - +
266A LEU* 2.9 28.9 + - - +
392A ASP* 3.9 37.7 - - + +
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Residues in contact with TYR 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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182A VAL* 4.1 19.5 - - + +
183A PRO* 3.7 26.0 - - + -
259A TRP* 2.7 57.3 + + + +
260A ALA 3.6 4.9 - - - +
262A ALA* 1.3 70.9 - - - +
264A ASN* 1.3 69.4 + - + +
266A LEU* 3.1 6.9 + - + +
267A ILE* 3.1 54.8 + - + +
276A VAL* 3.7 25.5 - - + +
280A GLN* 3.2 29.1 + - - -
322A TRP* 5.0 1.8 - + - -
324A ASP* 5.8 0.2 - - - -
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Residues in contact with ASN 264 (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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260A ALA 3.1 11.5 + - - +
261A LYS* 3.3 11.6 + - + +
263A TYR* 1.3 84.1 - - + +
265A ASN* 1.3 60.8 + - - +
267A ILE* 3.5 20.2 - - - +
268A LYS* 3.5 28.2 + - - +
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Residues in contact with ASN 265 (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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261A LYS* 3.2 12.6 + - + +
262A ALA* 3.6 9.6 + - - +
263A TYR 3.1 0.6 - - - -
264A ASN* 1.3 73.9 - - - +
266A LEU* 1.3 69.2 + - - +
268A LYS* 3.0 45.6 + - - +
269A ASP 4.5 0.2 + - - -
386A THR* 4.7 1.0 + - - -
388A GLU* 3.3 40.9 + - - +
389A ILE* 3.6 27.2 - - - +
392A ASP* 4.2 6.9 + - - +
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Residues in contact with LEU 266 (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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248A VAL* 3.9 31.9 - - + -
251A LEU* 4.6 4.7 - - + -
259A TRP* 4.1 25.1 - - + -
262A ALA 2.9 17.5 + - - +
263A TYR* 3.4 7.4 - - + +
265A ASN* 1.3 81.7 - - - +
267A ILE* 1.3 56.6 + - - +
268A LYS 3.3 3.3 + - - -
269A ASP* 3.8 2.8 + - - +
272A ASN* 3.0 53.8 + - + +
276A VAL* 4.0 22.7 - - + -
322A TRP* 4.2 2.7 - - + -
383A PHE* 4.1 7.6 - - + -
385A ILE* 5.9 0.2 - - + -
389A ILE* 4.3 21.5 - - + +
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Residues in contact with ILE 267 (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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263A TYR* 3.3 59.7 - - + +
264A ASN* 3.5 17.9 - - - +
266A LEU* 1.3 75.8 - - + +
268A LYS* 1.3 53.4 + - - +
269A ASP 3.1 2.9 - - - -
273A ARG* 2.7 60.6 + - + +
276A VAL* 4.1 20.9 - - + -
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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