Contacts of the helix formed by residues 296 - 310 (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 SER 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B VAL* 1.3 73.7 - - - +
297B ASP* 1.3 65.9 + - - +
298B ASP* 2.7 22.6 + - - -
299B VAL* 3.0 30.8 + - - +
300B TYR 3.1 9.7 + - - -
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Residues in contact with ASP 297 (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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294B ARG* 3.7 26.4 + - - -
295B VAL 3.4 0.8 + - - -
296B SER* 1.3 71.3 - - - +
298B ASP* 1.3 61.5 + - - +
299B VAL 3.2 0.9 + - - -
300B TYR* 3.3 22.8 + - - +
301B ARG 4.6 1.2 + - - -
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Residues in contact with ASP 298 (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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296B SER* 2.7 33.3 + - - -
297B ASP* 1.3 78.4 - - - +
299B VAL* 1.3 69.1 + - - +
300B TYR 3.6 0.2 - - - -
301B ARG* 5.3 1.4 + - - +
302B ASN* 4.3 8.3 + - - -
410B MET* 5.9 1.2 - - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B VAL* 4.0 4.0 - - + -
296B SER* 3.0 34.4 + - - +
298B ASP* 1.3 98.3 - - - +
300B TYR* 1.3 66.4 + - - +
301B ARG 3.4 1.8 - - - -
302B ASN* 3.1 18.5 + - + +
303B HIS* 2.9 47.4 + - + +
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Residues in contact with TYR 300 (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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126B LYS* 3.0 29.4 + - + -
294B ARG* 5.3 10.1 - - - -
295B VAL* 3.9 20.9 - - + +
296B SER 3.1 9.6 + - - +
297B ASP* 3.3 21.4 + - - +
299B VAL* 1.3 75.9 - - - +
301B ARG* 1.3 75.3 + - + +
303B HIS* 3.0 7.0 + - + +
304B VAL* 3.0 42.6 + - + +
334B ASP* 2.7 28.6 + - - -
336B SER* 2.8 16.1 + - - -
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Residues in contact with ARG 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 3.7 33.7 - - + +
297B ASP 4.6 1.6 + - - -
298B ASP 5.3 1.1 + - - +
299B VAL 3.4 0.6 - - - -
300B TYR* 1.3 86.2 - - + +
302B ASN* 1.3 63.8 + - - +
304B VAL* 3.3 9.4 + - + +
305B ALA* 3.0 24.1 + - - +
411B MET* 3.6 46.3 - - + +
412B LEU 5.6 1.2 - - - +
413B THR* 4.0 22.1 + - - -
563B VAL* 3.8 7.7 - - - +
586B ASN* 5.5 6.7 - - - +
587B PHE 5.4 1.0 + - - -
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Residues in contact with ASN 302 (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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298B ASP 4.3 5.3 + - - -
299B VAL* 3.1 27.8 + - + +
301B ARG* 1.3 77.3 - - - +
303B HIS* 1.3 65.6 + - + +
305B ALA* 3.5 3.5 + - - +
306B GLY* 3.1 17.5 + - - -
409B ILE* 3.5 33.7 + - + +
410B MET* 3.9 21.4 - - - +
411B MET* 2.7 38.5 + - - +
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B VAL* 3.9 30.4 - - + +
299B VAL* 2.9 47.7 + - + +
300B TYR* 3.0 10.3 + - + +
302B ASN* 1.3 77.5 - - + +
304B VAL* 1.3 60.8 + - + +
306B GLY* 3.0 3.7 + - - +
307B GLN* 2.9 27.1 + - - +
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Residues in contact with VAL 304 (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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123B ILE* 3.8 20.0 - - + -
300B TYR* 3.0 48.9 + - + +
301B ARG* 3.3 10.1 + - + +
303B HIS* 1.3 76.0 - - + +
305B ALA* 1.3 62.5 + - - +
307B GLN* 2.9 23.0 + - - +
308B MET* 3.0 36.8 + - + +
334B ASP* 5.2 0.9 - - - +
336B SER* 3.8 20.2 - - - +
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Residues in contact with ALA 305 (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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123B ILE* 4.8 3.0 - - + +
301B ARG 3.0 17.0 + - - +
302B ASN 3.7 4.7 - - - +
304B VAL* 1.3 76.7 - - - +
306B GLY* 1.3 58.1 + - - +
308B MET* 3.3 0.8 + - - -
309B LEU* 2.9 25.9 + - - +
409B ILE* 4.3 9.9 - - + -
411B MET* 3.7 28.7 - - + -
565B PHE* 3.1 35.5 - - + -
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Residues in contact with GLY 306 (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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302B ASN 3.1 11.4 + - - -
303B HIS* 3.0 8.7 + - - -
305B ALA* 1.3 78.3 - - - +
307B GLN* 1.3 56.8 + - - +
309B LEU* 4.5 0.4 - - - -
310B HIS* 2.9 55.3 + - - -
311B GLY 3.1 5.0 + - - -
312B GLY* 4.4 1.1 - - - -
409B ILE* 4.1 8.2 - - - +
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Residues in contact with GLN 307 (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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289B ASP* 2.7 40.5 - - - +
290B LYS 4.9 1.0 - - - +
292B VAL* 4.9 14.7 - - + +
303B HIS 2.9 10.9 + - - +
304B VAL* 2.9 21.2 + - - +
306B GLY* 1.3 76.3 - - - +
308B MET* 1.3 68.6 + - - +
311B GLY* 3.1 28.0 + - - +
312B GLY* 4.2 2.0 - - - +
317B ASN* 3.5 10.2 + - - +
321B ARG* 3.0 26.0 + - - +
330B ILE* 5.0 2.2 - - - -
332B ALA* 3.8 22.4 - - - +
334B ASP* 5.7 2.0 + - - -
336B SER* 5.1 1.4 - - - -
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Residues in contact with MET 308 (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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121B GLY* 4.4 0.2 - - - -
122B VAL 3.1 23.6 - - - +
123B ILE* 4.5 2.5 - - + -
304B VAL* 3.0 38.7 + - + +
305B ALA* 4.5 0.2 - - - -
307B GLN* 1.3 85.4 - - - +
309B LEU* 1.3 62.0 + - - +
321B ARG* 5.2 0.9 + - - -
330B ILE* 3.7 39.6 - - + +
332B ALA* 5.5 0.7 - - + -
336B SER* 4.5 3.6 - - - -
337B CYS* 3.4 32.5 - - - +
338B GLY* 3.5 7.0 - - - -
339B MET 3.6 7.5 - - - +
340B VAL* 3.3 25.8 - - - +
565B PHE* 3.7 23.3 - - + -
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Residues in contact with LEU 309 (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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115B VAL* 3.9 6.2 - - - +
116B ILE* 4.0 25.2 + - + -
119B SER 3.5 25.2 - - - +
121B GLY* 3.8 15.3 - - - +
305B ALA 2.9 17.3 + - - +
306B GLY 4.0 1.3 - - - +
308B MET* 1.3 81.3 - - - +
310B HIS* 1.3 61.0 + - - +
323B PHE* 3.8 15.2 - - - -
340B VAL* 4.1 6.2 - - + +
407B LEU* 3.5 33.0 - - + -
409B ILE* 4.2 9.0 - - + -
565B PHE* 3.7 21.5 - - + +
566B PHE* 4.5 6.1 - - - -
567B GLY 4.9 6.5 - - - +
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.6 23.1 - - + +
116B ILE* 4.0 8.6 - - + +
306B GLY* 2.9 35.8 + - - -
309B LEU* 1.3 75.7 - - - +
311B GLY* 1.3 54.1 + - - +
312B GLY* 2.9 34.9 + - - -
318B SER* 2.6 28.9 + - - -
321B ARG* 5.1 0.2 - - - -
323B PHE* 3.8 14.4 - - - -
400B LEU* 4.5 4.3 - - + +
404B ILE* 3.5 45.3 - - + +
407B LEU* 3.8 29.5 - - + +
409B ILE* 4.6 2.0 - - + -
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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