Contacts of the helix formed by residues 329 - 339 (chain B) in PDB entry 3H44
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 ASN 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B LEU* 5.4 4.8 + - - +
325B TYR 2.8 12.1 + - - -
326B TYR* 3.5 18.4 + - - +
328B SER* 1.3 79.3 + - - +
330B PRO* 1.3 66.5 - - - +
331B GLY 3.1 4.3 + - - +
332B HIS* 3.2 27.1 + - + +
333B TYR* 3.4 9.5 + - - +
363B GLN* 3.5 26.7 + - - +
456B LEU* 3.9 19.0 - - + +
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Residues in contact with PRO 330 (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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322B LEU* 4.5 11.0 - - + +
325B TYR* 3.8 20.2 - - + -
328B SER* 3.4 10.9 - - - +
329B ASN* 1.3 89.1 - - - +
331B GLY* 1.3 61.9 + - - +
333B TYR* 3.4 5.0 + - + +
334B LEU* 3.1 29.2 + - - +
463B LEU* 3.8 18.4 - - + +
464B ILE* 3.8 40.8 - - + +
467B VAL* 4.1 15.5 - - + -
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Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 4.0 13.5 - - - +
329B ASN* 3.1 3.0 - - - +
330B PRO* 1.3 79.6 - - - +
332B HIS* 1.3 58.7 + - - +
334B LEU* 3.4 3.8 + - - -
335B GLY* 3.0 26.2 + - - -
363B GLN* 3.3 30.4 + - - -
373B PHE* 4.1 11.6 - - - -
467B VAL* 5.3 0.4 - - - -
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Residues in contact with HIS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASN* 3.2 28.6 + - + +
331B GLY* 1.3 72.9 - - - +
333B TYR* 1.3 69.8 + - - +
335B GLY* 3.3 1.2 + - - -
336B HIS* 2.8 28.2 + - + +
363B GLN* 3.0 13.4 - - - +
414B LEU* 4.1 27.4 - - + +
418B ASN* 4.8 16.5 + - - -
456B LEU* 4.3 16.5 - - + +
2D SER* 4.0 19.3 + - - -
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Residues in contact with TYR 333 (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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329B ASN 3.4 8.4 + - - +
330B PRO 3.4 8.7 + - - +
331B GLY 3.3 0.2 - - - -
332B HIS* 1.3 81.1 + - - +
334B LEU* 1.3 75.8 + - + +
336B HIS* 3.2 10.8 + - - +
337B LEU* 3.0 39.0 + - + +
401B LEU* 5.8 3.1 - - + +
405B GLY 4.9 0.5 + - - -
406B PRO* 3.5 6.7 - - + +
407B GLN* 3.0 50.4 + - - +
410B VAL* 3.8 20.5 - - + +
411B PHE* 4.3 22.7 - + + -
414B LEU* 4.7 8.3 - - + -
459B PHE* 4.5 4.7 - + - -
464B ILE* 3.4 42.2 - - + -
524B LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PRO 3.1 16.3 + - - +
331B GLY* 4.1 3.1 - - - +
332B HIS 3.2 0.2 - - - -
333B TYR* 1.3 97.5 - - + +
335B GLY* 1.3 65.6 + - - +
337B LEU* 3.2 4.0 + - - +
338B ILE* 2.9 33.3 + - + +
373B PHE* 4.1 13.9 - - + -
401B LEU* 4.2 14.1 - - + -
464B ILE* 4.0 11.2 - - + +
467B VAL* 3.5 37.7 - - + -
468B LEU* 3.9 37.9 - - + +
471B LEU* 4.9 4.0 - - + -
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Residues in contact with GLY 335 (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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331B GLY 3.0 13.7 + - - -
332B HIS* 3.8 1.6 - - - -
334B LEU* 1.3 76.2 - - - +
336B HIS* 1.3 57.7 + - - +
338B ILE* 4.7 0.4 - - - -
339B GLY* 2.8 30.2 + - - -
361B GLY 3.8 4.1 - - - +
362B GLY* 3.4 32.8 - - - -
373B PHE* 4.0 2.6 - - - -
2D SER* 3.7 10.8 + - - -
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B HIS* 2.8 24.4 + - - +
333B TYR 3.5 3.8 - - - +
334B LEU 3.1 0.2 - - - -
335B GLY* 1.3 77.0 - - - +
337B LEU* 1.3 78.1 + - + +
339B GLY 3.9 0.5 - - - -
340B HIS* 3.1 41.2 + + - +
410B VAL* 4.2 7.7 - - + +
413B GLU* 5.4 6.9 + - - -
414B LEU* 3.4 45.8 - - + +
525B PRO* 4.9 2.8 - - - +
609B TYR* 5.0 2.8 + - - -
613B LEU* 3.7 31.9 - - + +
2D SER* 3.8 13.7 + - - +
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Residues in contact with LEU 337 (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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333B TYR* 3.0 61.9 - - + +
334B LEU* 3.2 6.7 + - + +
336B HIS* 1.3 88.2 - - + +
338B ILE* 1.3 66.8 + - - +
339B GLY 3.1 1.1 - - - -
340B HIS* 3.0 17.7 + - - +
345B SER* 5.2 0.5 - - - -
346B LEU 5.6 0.2 + - - -
397B TYR* 3.2 24.7 + - - +
401B LEU* 4.1 25.1 - - + -
410B VAL* 4.1 14.6 - - + -
524B LEU* 4.5 6.1 - - + -
525B PRO* 3.8 27.8 - - + -
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Residues in contact with ILE 338 (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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334B LEU* 2.9 25.6 + - + +
335B GLY* 4.3 3.1 - - - +
337B LEU* 1.3 72.9 - - - +
339B GLY* 1.3 60.2 + - - +
340B HIS 3.5 4.0 + - - +
346B LEU* 4.4 18.9 + - + +
347B LEU 5.3 0.2 + - - -
359B LEU* 3.7 11.4 - - - +
361B GLY* 4.9 4.7 - - - -
373B PHE* 4.2 17.3 - - + -
375B ILE* 3.6 38.1 - - + -
397B TYR* 4.0 13.4 - - + -
398B ILE* 3.8 26.5 - - + -
401B LEU* 3.8 24.2 - - + -
468B LEU* 5.7 0.2 - - + -
471B LEU* 5.1 4.3 - - + -
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLY 2.8 22.9 + - - -
336B HIS 3.9 2.9 - - - -
338B ILE* 1.3 71.9 - - - +
340B HIS* 1.3 65.4 + - - +
341B GLU* 3.6 1.4 + - - +
359B LEU* 4.0 10.2 - - - +
361B GLY* 4.5 4.4 - - - -
609B TYR* 3.4 8.7 + - - -
1D ALA* 3.1 40.9 + - - -
2D SER 4.5 0.2 - - - -
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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