Contacts of the helix formed by residues 379 - 385 (chain B) in PDB entry 3N9Y
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 ALA 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B HIS* 4.5 16.2 - - + +
43B PHE* 3.4 36.6 - - + -
61B TYR* 5.2 4.0 - - + -
62B VAL 2.9 10.8 + - - +
63B ILE* 4.4 2.0 - - + +
353B VAL 4.1 4.7 - - - -
354B THR* 4.2 5.6 - - + -
377B GLN 3.8 1.2 + - - -
378B VAL* 1.3 69.3 - - - +
380B ILE* 1.3 53.7 + - - +
381B TYR 3.3 2.9 - - - -
382B ALA* 3.2 8.6 + - + +
383B LEU* 2.8 36.5 + - - +
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU 5.1 2.7 - - - +
347B ARG* 4.8 2.5 - - - +
350B PRO* 3.6 26.5 - - + -
352B SER* 3.7 6.5 - - - +
353B VAL 3.1 9.2 + - - +
354B THR 4.1 2.2 - - - -
355B LEU* 3.7 29.4 - - + +
378B VAL* 2.9 25.3 + - + +
379B ALA* 1.3 70.7 - - - +
381B TYR* 1.3 62.6 + - - +
383B LEU* 3.4 6.8 + - + +
384B GLY* 3.1 19.8 + - - -
414B LEU* 3.6 43.3 - - + +
415B GLY* 5.0 12.6 - - - -
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Residues in contact with TYR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 3.6 56.9 - + + -
37B LEU* 4.3 9.9 - - + +
39B HIS* 5.7 0.9 - - - +
40B VAL* 3.9 16.2 - - + -
347B ARG 5.0 0.9 - - - +
348B LEU 4.1 2.2 - - - -
349B HIS* 5.8 0.2 - - - -
350B PRO* 3.9 29.6 - - + -
353B VAL* 3.2 16.6 + - + +
380B ILE* 1.3 80.2 - - - +
382B ALA* 1.3 65.0 + - - +
384B GLY* 3.2 9.9 + - - -
385B ARG* 3.3 68.4 + - + +
456B THR* 4.5 12.3 + - + -
462B LEU* 4.2 7.4 - - + -
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 4.4 3.7 - - + +
40B VAL* 4.0 31.5 - - + +
43B PHE* 3.9 18.4 - - + -
63B ILE* 3.7 18.4 - - + +
379B ALA* 3.2 15.3 + - + +
381B TYR* 1.3 75.7 - - - +
383B LEU* 1.3 66.6 + - - +
385B ARG* 3.2 13.3 + - - +
386B GLU* 3.2 14.9 + - - +
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Residues in contact with LEU 383 (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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63B ILE* 3.5 36.0 - - + +
65B PRO* 4.0 16.6 - - + -
68B VAL* 4.9 2.0 - - + -
378B VAL* 4.8 7.6 - - + -
379B ALA 2.8 20.2 + - - +
380B ILE* 3.4 8.3 - - + +
382B ALA* 1.3 72.4 - - - +
384B GLY* 1.3 62.4 + - - +
386B GLU* 3.0 15.6 + - - +
389B PHE* 3.7 29.4 - - + -
390B PHE* 3.5 20.4 - - + -
411B PHE 4.5 1.6 - - - +
412B ARG* 5.1 4.5 - - + +
414B LEU* 4.0 27.8 - - + -
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Residues in contact with GLY 384 (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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347B ARG* 2.7 61.4 + - - -
380B ILE 3.1 12.0 + - - -
381B TYR 3.2 3.4 + - - -
383B LEU* 1.3 76.9 - - - +
385B ARG* 1.3 63.8 + - - +
386B GLU 3.4 0.2 - - - -
390B PHE* 3.9 7.4 - - - -
393B PRO* 3.7 4.2 - - - +
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Residues in contact with ARG 385 (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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40B VAL* 5.3 6.5 - - + -
347B ARG 5.0 0.4 + - - -
348B LEU* 2.8 51.5 + - - +
349B HIS* 3.9 17.6 + - - -
381B TYR* 3.3 57.6 + - + +
382B ALA* 3.2 8.1 + - - +
383B LEU 3.1 0.6 - - - -
384B GLY* 1.3 78.9 - - - +
386B GLU* 1.3 58.5 + - - +
387B PRO* 3.2 12.8 - - - +
393B PRO* 3.5 15.5 - - - +
394B GLU* 3.5 33.4 + - - +
456B THR* 4.3 5.9 + - - -
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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