Contacts of the helix formed by residues 330 - 339 (chain B) in PDB entry 2E4Y
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 VAL 330 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PHE* 4.3 7.9 - - + -
328B HIS 4.5 2.0 - - - +
329B PRO* 1.3 70.5 - - - +
331B ARG* 1.3 66.2 + - - +
332B GLN 4.2 1.6 - - - +
333B PHE* 3.0 33.8 + - + +
334B ASP* 3.4 3.6 + - - -
386B GLN* 2.9 19.4 + - - +
390B ILE* 4.8 1.1 - - + -
391B MET* 4.0 32.1 - - + -
394B VAL* 4.6 13.7 - - + -
395B ASN* 6.0 0.7 - - - +
444B PHE* 3.6 38.4 - - + +
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Residues in contact with ARG 331 (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 PRO 3.3 10.1 + - - +
330B VAL* 1.3 70.6 - - - +
332B GLN* 1.3 75.4 + - - +
334B ASP* 2.9 33.5 + - - +
335B ARG* 3.6 3.1 + - - +
444B PHE 4.1 6.8 + - - +
446B PRO* 6.0 5.4 - - + -
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 3.7 22.2 - - + -
78B GLU* 5.4 1.8 - - - +
330B VAL* 3.4 0.6 - - + -
331B ARG* 1.3 84.5 + - - +
333B PHE* 1.3 64.9 + - - +
334B ASP 3.1 0.3 + - - -
335B ARG* 3.1 18.5 + - - +
336B TYR* 2.9 21.1 + - - +
443B PRO 4.2 5.1 + - - -
444B PHE* 3.5 46.8 - - + +
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Residues in contact with PHE 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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67B GLN* 3.6 45.1 - - + -
70B GLU* 3.9 3.4 - - + -
71B ALA* 3.2 37.0 - - + -
74B PHE* 3.8 15.4 - + + -
330B VAL* 3.0 27.4 + - + +
332B GLN* 1.3 76.5 - - - +
334B ASP* 1.3 54.9 + - - +
336B TYR* 3.0 26.8 + + - +
337B PHE* 2.7 47.2 + + + +
384B TYR* 3.9 9.9 - - - -
386B GLN* 3.4 17.9 - - - +
390B ILE* 3.8 16.6 - - + -
394B VAL* 5.7 0.2 - - + -
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Residues in contact with ASP 334 (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 PRO* 4.7 7.1 - - - +
330B VAL 3.4 3.7 + - - +
331B ARG* 2.9 24.3 + - - +
333B PHE* 1.3 81.1 - - - +
335B ARG* 1.3 64.2 + - - +
337B PHE* 3.9 0.9 - - - +
338B GLN* 3.0 38.6 + - - +
384B TYR* 2.5 36.5 + - - -
386B GLN* 3.3 21.7 + - - +
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Residues in contact with ARG 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 ARG 3.6 3.0 + - - +
332B GLN* 3.1 19.4 + - - +
334B ASP* 1.3 78.8 - - - +
336B TYR* 1.3 63.6 + - - +
338B GLN* 3.6 8.3 + - - +
339B SER* 3.1 27.7 + - - -
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Residues in contact with TYR 336 (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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70B GLU* 2.7 35.8 + - + -
73B LEU* 4.0 1.4 - - - +
74B PHE* 3.2 46.7 - + + -
77B ASP* 4.6 6.5 - - - -
332B GLN 2.9 12.4 + - - +
333B PHE* 3.2 22.4 - + - +
335B ARG* 1.3 79.5 - - - +
337B PHE* 1.3 65.3 + - - +
339B SER* 2.5 29.7 + - - -
340B LEU* 3.7 21.4 + - + +
347B ARG* 2.8 26.9 + - - -
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Residues in contact with PHE 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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62B GLU 5.5 1.1 - - - -
63B ASP* 5.7 0.2 - - - -
66B ILE* 4.1 13.0 - - + -
67B GLN* 3.8 20.4 - - + -
70B GLU* 4.0 21.3 - - + -
333B PHE* 2.7 34.5 + + + +
334B ASP 4.0 1.6 - - - +
336B TYR* 1.3 74.9 - - - +
338B GLN* 1.3 56.7 + - - +
340B LEU* 2.8 54.6 + - + +
351B PHE* 4.6 2.2 - + - -
354B PHE* 3.9 24.5 - + - -
358B LYS* 5.5 3.1 - - - -
379B ILE* 4.0 23.1 - - + +
384B TYR* 3.6 42.0 - + + +
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Residues in contact with GLN 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 ASP* 3.0 34.5 + - - +
335B ARG* 3.8 7.1 - - - +
337B PHE* 1.3 74.1 - - - +
339B SER* 1.3 59.0 + - - +
340B LEU 3.2 5.4 + - - +
378B ALA* 5.4 2.8 - - - +
379B ILE* 3.0 30.7 + - - +
380B ASP* 3.0 29.0 - - - +
381B SER* 3.1 11.2 + - - +
384B TYR* 3.3 32.9 - - + -
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Residues in contact with SER 339 (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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335B ARG* 3.1 17.4 + - - -
336B TYR* 2.5 27.2 + - - -
337B PHE 2.9 1.6 + - - -
338B GLN* 1.3 76.2 - - - +
340B LEU* 1.3 62.5 + - - +
341B ASN* 4.0 1.6 - - - +
344B ASN* 3.2 20.6 + - - -
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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