Contacts of the helix formed by residues 329 - 339 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A LEU* 6.1 0.6 - - - +
325A TYR 2.7 16.7 + - - +
326A TYR* 3.6 22.8 - - - +
328A SER* 1.3 74.8 + - - +
330A PRO* 1.3 57.5 - - - +
331A GLY 2.5 13.2 + - - +
332A HIS* 2.8 37.7 + - + +
333A TYR* 3.9 1.5 + - - -
363A GLN* 3.4 17.1 + - - +
456A LEU* 3.8 15.1 - - + +
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Residues in contact with PRO 330 (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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322A LEU* 4.4 8.7 - - + -
325A TYR* 3.7 25.8 - - + -
328A SER* 3.6 8.6 - - - +
329A ASN* 1.3 89.1 - - - +
331A GLY* 1.3 63.2 + - - +
332A HIS 3.3 0.2 - - - -
333A TYR* 3.3 8.7 + - + +
334A LEU* 3.2 25.8 + - - +
460A ARG* 5.3 0.7 - - + +
463A LEU* 3.8 18.4 - - + +
464A ILE* 3.7 39.1 - - + +
467A VAL* 4.1 15.0 - - + -
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Residues in contact with GLY 331 (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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322A LEU* 4.0 9.9 - - - +
329A ASN* 2.5 10.3 + - - +
330A PRO* 1.3 80.1 - - - +
332A HIS* 1.3 54.8 + - - -
334A LEU* 3.5 5.9 + - - -
335A GLY* 2.9 24.4 + - - -
363A GLN* 3.4 32.3 + - - -
373A PHE* 4.1 10.7 - - - -
467A VAL* 5.3 1.1 - - - -
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Residues in contact with HIS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ASN* 2.8 37.1 + - + +
331A GLY* 1.3 68.5 - - - -
333A TYR* 1.3 54.7 + - - +
335A GLY* 3.0 1.8 + - - -
336A HIS* 2.6 45.4 + - + +
363A GLN* 3.6 7.5 - - - +
414A LEU* 4.0 23.2 - - + +
418A ASN* 4.4 13.6 + - - -
456A LEU* 4.5 18.8 - - + -
2C SER* 3.8 18.7 + - - -
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Residues in contact with TYR 333 (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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329A ASN 3.9 2.1 + - - +
330A PRO* 3.3 14.5 + - + +
332A HIS* 1.3 79.7 - - - +
334A LEU* 1.3 70.6 + - + +
336A HIS* 3.5 3.8 + - - +
337A LEU* 3.2 44.7 + - + +
401A LEU* 5.8 0.7 - - + -
405A GLY 4.4 1.2 + - - -
406A PRO* 3.6 6.1 - - + +
407A GLN* 2.7 53.5 + - - +
410A VAL* 3.9 15.7 - - + -
411A PHE* 4.3 16.6 - + + -
414A LEU* 4.3 17.3 - - + -
459A PHE* 4.9 0.9 - + - -
464A ILE* 3.8 44.2 - - + -
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Residues in contact with LEU 334 (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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330A PRO 3.2 14.0 + - - +
331A GLY 4.1 0.2 - - - +
333A TYR* 1.3 94.3 - - + +
335A GLY* 1.3 58.3 + - - +
337A LEU* 4.6 1.6 - - - -
338A ILE* 2.7 45.0 + - + +
373A PHE* 3.9 14.6 - - + -
401A LEU* 4.0 16.8 - - + -
464A ILE* 3.9 9.6 - - + +
467A VAL* 3.6 34.5 - - + -
468A LEU* 3.8 45.8 - - + +
471A LEU* 4.6 4.9 - - + -
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Residues in contact with GLY 335 (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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331A GLY 2.9 16.1 + - - -
332A HIS* 3.0 3.8 + - - -
334A LEU* 1.3 74.2 - - - +
336A HIS* 1.3 64.7 + - - +
339A GLY* 2.8 25.9 + - - -
361A GLY 3.7 3.2 - - - +
362A GLY* 3.7 24.9 - - - -
373A PHE* 4.3 0.8 - - - -
2C SER* 3.4 14.6 + - - -
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Residues in contact with HIS 336 (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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332A HIS* 2.6 26.6 + - + +
333A TYR 3.6 4.5 - - - +
334A LEU 3.4 0.2 - - - -
335A GLY* 1.3 73.5 - - - +
337A LEU* 1.3 83.5 + - + +
339A GLY 4.0 0.9 - - - -
340A HIS* 3.2 50.5 + + - +
410A VAL* 3.9 13.4 - - + +
413A GLU* 5.3 9.1 + - + +
414A LEU* 3.6 36.5 - - + +
525A PRO* 5.0 2.8 - - - +
609A TYR* 5.1 2.6 + - - -
613A LEU* 3.7 28.3 - - + +
2C SER* 3.4 11.1 + - - -
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Residues in contact with LEU 337 (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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333A TYR* 3.2 49.8 + - + +
334A LEU 3.8 2.2 - - - +
335A GLY 3.2 0.6 - - - -
336A HIS* 1.3 103.6 - - + +
338A ILE* 1.3 68.3 + - - +
340A HIS* 3.1 15.7 + - - +
346A LEU 5.6 0.2 + - - -
397A TYR* 3.0 22.6 + - - +
401A LEU* 4.2 30.7 - - + -
407A GLN* 6.3 0.4 - - + -
410A VAL* 4.0 15.9 - - + -
524A LEU* 5.2 6.1 - - + -
525A PRO* 4.0 24.2 - - + -
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Residues in contact with ILE 338 (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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334A LEU* 2.7 41.6 + - + +
335A GLY* 4.7 0.4 - - - +
337A LEU* 1.3 74.4 - - - +
339A GLY* 1.3 57.7 + - - +
340A HIS 3.2 7.4 + - - +
346A LEU* 4.2 26.5 + - + +
359A LEU* 3.9 7.1 - - - +
361A GLY* 4.8 5.8 - - - -
373A PHE* 3.6 24.9 - - + -
375A ILE* 3.8 38.1 - - + -
397A TYR* 3.8 20.9 - - + -
398A ILE* 4.9 11.0 - - + -
401A LEU* 4.2 13.5 - - + -
468A LEU* 5.3 1.1 - - + -
471A LEU* 4.4 9.0 - - + -
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Residues in contact with GLY 339 (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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335A GLY 2.8 20.6 + - - -
336A HIS 4.0 2.7 - - - -
338A ILE* 1.3 71.0 - - - +
340A HIS* 1.3 65.5 + - - +
341A GLU* 3.7 0.9 - - - +
359A LEU* 3.8 14.6 - - - +
361A GLY 4.3 4.9 + - - -
609A TYR* 3.7 3.5 + - - -
1C ALA 2.9 44.8 + - - -
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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