Contacts of the helix formed by residues 339 - 349 (chain B) in PDB entry 4O9U
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 GLY 339 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ILE* 6.0 0.2 - - - -
332B PRO 4.6 1.6 + - - -
334B ALA 5.4 0.8 + - - -
337B MET* 3.4 1.9 + - - +
338B PRO* 1.3 72.1 - - - +
340B HIS* 1.3 63.9 + - - +
341B MET 3.3 2.9 - - - -
342B ASN* 3.3 31.1 + - - +
343B VAL* 3.5 19.6 + - - +
158F LEU* 4.7 6.7 - - - +
159F THR 3.3 24.3 + - - -
160F THR* 3.8 3.2 - - - +
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Residues in contact with HIS 340 (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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301B TYR* 3.9 21.5 - + - -
304B ALA* 3.6 12.3 - - - +
334B ALA 3.6 14.8 + - - +
335B GLY* 4.1 0.4 - - - -
336B ARG* 3.2 20.7 + - + -
337B MET* 3.2 36.7 + - + +
338B PRO 3.2 2.2 - - - -
339B GLY* 1.3 76.1 - - - +
341B MET* 1.3 69.9 + - + +
343B VAL* 3.1 20.8 - - - +
344B LEU* 3.5 23.2 - - + +
180E LEU* 5.9 2.0 - - + -
205E GLN* 4.8 2.5 - - + -
208E SER* 3.4 26.6 + - - -
209E LEU* 4.2 11.9 - - + +
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Residues in contact with MET 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO* 3.6 32.1 - - + +
300B GLY 3.3 31.9 - - - +
303B MET* 3.8 19.3 - - + -
304B ALA* 4.5 3.4 - - + -
330B ILE* 4.0 26.4 - - + +
334B ALA* 4.0 24.7 + - + +
335B GLY* 4.4 5.8 - - - -
339B GLY 3.3 0.2 - - - -
340B HIS* 1.3 99.4 - - + +
342B ASN* 1.3 57.5 + - - +
343B VAL 3.2 0.4 - - - -
344B LEU* 3.0 6.1 + - + +
345B LEU* 2.7 40.7 + - + +
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Residues in contact with ASN 342 (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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330B ILE* 3.7 13.6 - - - +
339B GLY* 3.3 17.4 + - - +
341B MET* 1.3 76.1 - - - +
343B VAL* 1.3 57.3 + - - +
345B LEU* 3.9 5.6 - - - +
346B ALA* 3.0 29.3 + - - +
352B TYR* 4.7 4.8 - - + -
355B LEU* 4.9 5.9 - - + +
157F MET* 3.3 40.5 - - - +
158F LEU* 3.6 5.6 - - + +
159F THR* 2.8 55.4 + - - +
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Residues in contact with VAL 343 (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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337B MET* 4.2 8.7 - - + -
339B GLY 3.5 12.3 + - - +
340B HIS 3.1 22.0 - - - +
342B ASN* 1.3 76.7 - - - +
344B LEU* 1.3 60.9 + - + +
345B LEU 3.2 0.2 - - - -
346B ALA* 3.3 2.6 + - - +
347B GLU* 3.0 28.4 + - - +
181E MET* 6.5 0.7 - - - -
184E ALA* 4.9 14.1 - - + -
188E ARG* 3.5 33.7 + - + +
209E LEU* 4.1 22.0 - - + -
158F LEU* 4.2 13.9 - - + -
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Residues in contact with LEU 344 (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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303B MET* 3.5 32.5 - - + -
304B ALA* 3.9 5.6 - - + -
307B GLN* 5.1 2.2 - - - +
309B GLN* 3.2 37.4 - - - +
340B HIS* 3.5 34.5 - - + +
341B MET 3.0 6.5 + - - +
343B VAL* 1.3 80.8 - - + +
345B LEU* 1.3 60.4 + - - +
347B GLU* 3.7 22.0 - - - +
348B ALA 3.7 8.5 + - - -
208E SER 3.6 24.9 - - - +
209E LEU* 4.0 18.2 - - + +
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Residues in contact with LEU 345 (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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299B PRO* 4.6 5.6 - - + -
303B MET* 5.0 6.3 - - - -
309B GLN* 4.8 12.6 - - + +
312B LEU* 4.3 22.9 - - + -
313B LYS* 5.8 0.7 - - + -
328B PHE* 4.3 18.8 - - + -
330B ILE* 3.7 31.2 - - + -
341B MET* 2.7 19.2 + - + +
342B ASN* 4.2 4.5 - - - +
344B LEU* 1.3 81.2 - - - +
346B ALA* 1.3 59.8 + - - +
347B GLU 3.1 1.1 - - - -
348B ALA* 3.8 1.3 + - - +
349B GLY 3.4 2.6 + - - -
350B VAL* 3.0 53.4 + - + +
355B LEU* 4.5 18.6 - - + -
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Residues in contact with ALA 346 (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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342B ASN 3.0 20.9 + - - +
343B VAL 3.3 6.0 + - - +
345B LEU* 1.3 76.9 - - - +
347B GLU* 1.3 62.2 + - - +
349B GLY* 3.6 9.0 + - - -
350B VAL 4.8 3.4 - - - -
352B TYR* 3.2 34.6 + - + +
188E ARG* 4.1 20.2 - - - +
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Residues in contact with GLU 347 (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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307B GLN* 5.6 0.7 - - - +
309B GLN* 4.6 6.2 + - - +
310B HIS* 3.4 28.5 + - + -
343B VAL 3.0 16.0 + - - +
344B LEU* 3.7 29.1 - - - +
345B LEU 3.1 0.2 - - - -
346B ALA* 1.3 75.6 - - - +
348B ALA* 1.3 65.5 + - - +
349B GLY* 3.0 3.4 + - - -
367D THR* 5.1 3.6 - - - +
403D LYS* 5.7 2.4 + - - -
187E LYS* 6.5 0.7 - - - -
209E LEU 4.5 6.4 - - - +
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Residues in contact with ALA 348 (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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309B GLN* 3.6 26.5 - - + +
310B HIS* 3.7 23.0 - - + +
313B LYS* 3.9 28.1 + - + +
344B LEU 3.7 10.2 + - - +
345B LEU* 3.8 4.9 + - - +
346B ALA 3.6 0.2 - - - -
347B GLU* 1.3 78.9 - - - +
349B GLY* 1.3 57.9 + - - +
350B VAL* 4.3 2.7 - - + -
367D THR* 4.8 8.0 - - - +
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Residues in contact with GLY 349 (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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313B LYS* 3.6 16.9 + - - -
345B LEU 3.4 2.2 + - - -
346B ALA 3.9 9.6 - - - -
347B GLU 3.0 5.2 - - - -
348B ALA* 1.3 79.2 - - - +
350B VAL* 1.3 65.7 + - - +
351B ASP* 3.4 3.1 + - - -
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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