Contacts of the helix formed by residues 247 - 254 (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 PRO 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B TYR* 3.7 30.5 - - + -
245B LYS 3.5 5.4 - - - +
246B GLU* 1.3 89.8 - - + +
248B VAL* 1.3 64.0 + - - +
249B GLY 3.1 3.4 - - - +
250B ILE* 3.0 31.0 + - + +
314B SER 5.4 2.9 - - - +
319B GLY* 3.7 25.8 - - - +
393B ILE* 3.9 9.1 - - + +
397B LYS* 3.8 27.4 - - - +
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Residues in contact with VAL 248 (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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209B TYR 5.2 2.4 + - - +
211B PHE* 5.4 1.6 - - + -
246B GLU* 2.8 18.1 + - + +
247B PRO* 1.3 71.2 - - - +
249B GLY* 1.3 63.2 + - - +
251B LEU* 3.0 36.4 + - + +
266B LEU* 4.1 21.1 - - + -
322B TRP* 4.3 6.2 - - + -
383B PHE* 3.9 40.6 - - + -
385B ILE* 3.6 30.7 - - + -
393B ILE* 4.0 11.7 - - + -
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Residues in contact with GLY 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TYR 5.5 0.2 + - - -
211B PHE* 4.3 9.9 - - - -
247B PRO* 3.1 2.0 - - - +
248B VAL* 1.3 78.8 - - - +
250B ILE* 1.3 54.0 + - - +
251B LEU 3.0 0.7 - - - -
252B THR* 2.5 35.2 + - - -
318B SER 4.8 0.9 - - - -
319B GLY 4.3 4.5 + - - -
321B ARG 3.1 25.3 - - - +
322B TRP* 3.7 18.2 - - - -
323B PHE* 4.7 0.9 - - - -
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Residues in contact with ILE 250 (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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247B PRO* 3.0 25.4 + - + +
249B GLY* 1.3 73.3 - - - +
251B LEU* 1.3 64.0 + - - +
252B THR 3.1 0.7 - - - -
253B SER* 2.6 28.1 + - - +
314B SER* 3.6 37.9 - - - -
318B SER* 4.0 15.5 - - - +
319B GLY* 4.2 12.6 - - - +
323B PHE* 5.7 0.2 - - - -
393B ILE* 4.0 19.1 - - + +
396B ALA* 3.5 22.1 - - + +
397B LYS* 4.1 9.4 - - + -
400B LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 251 (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* 3.0 34.4 + - + +
249B GLY 3.0 0.6 - - - -
250B ILE* 1.3 80.8 - - - +
252B THR* 1.3 55.4 - - - +
253B SER 3.1 5.0 + - - -
254B ASN* 3.3 17.8 + - - +
259B TRP* 3.4 38.7 - - + -
262B ALA* 4.6 9.2 - - + +
266B LEU* 4.3 14.4 - - + -
389B ILE* 4.7 5.2 - - + -
392B ASP* 3.4 46.4 - - + +
393B ILE* 3.5 21.1 - - + +
396B ALA* 4.0 6.1 - - + -
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Residues in contact with THR 252 (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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114B VAL* 4.0 3.5 - - - +
249B GLY 2.5 21.1 + - - +
251B LEU* 1.3 76.3 - - - +
253B SER* 1.3 57.8 + - - +
254B ASN 3.4 0.6 - - - +
256B ARG* 3.7 18.2 + - - -
259B TRP* 3.5 35.2 - - + +
322B TRP* 3.6 34.3 - - + +
323B PHE* 2.9 41.0 + - - +
324B ASP* 3.8 9.2 - - - +
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Residues in contact with SER 253 (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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113B PRO* 3.3 20.9 - - - +
115B VAL* 3.5 25.1 - - - +
250B ILE* 2.6 22.5 + - - +
252B THR* 1.3 77.8 + - - +
254B ASN* 1.3 60.0 + - - +
323B PHE* 4.1 10.1 - - - -
396B ALA 4.5 2.4 + - - -
399B ASN* 3.8 1.2 + - - -
400B LEU* 3.7 35.1 - - - +
403B MET* 3.8 12.3 - - - +
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Residues in contact with ASN 254 (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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113B PRO* 3.6 13.0 - - - +
251B LEU* 3.3 16.3 + - - +
252B THR 3.4 2.3 - - - +
253B SER* 1.3 82.6 + - - +
255B HIS* 1.3 87.9 + - - +
256B ARG* 3.4 8.3 + - - -
258B THR* 3.6 27.3 + - + +
259B TRP* 4.2 6.6 - - + +
392B ASP 4.9 1.2 + - - -
395B LYS* 4.0 8.9 + - - +
396B ALA* 3.5 32.2 - - + +
399B ASN* 3.1 27.4 + - - +
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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