Contacts of the helix formed by residues 330 - 339 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A PHE* 4.3 8.1 - - + -
328A HIS 4.5 1.6 - - - +
329A PRO* 1.3 69.2 - - - +
331A ARG* 1.3 66.1 + - - +
332A GLN 4.1 1.3 - - - +
333A PHE* 3.1 33.7 + - + +
334A ASP* 3.5 4.0 + - - -
386A GLN* 2.9 18.9 + - - +
390A ILE* 4.8 1.1 - - + -
391A MET* 4.0 32.3 - - + +
394A VAL* 4.5 13.7 - - + -
395A ASN* 6.1 0.4 - - - +
444A PHE* 3.7 37.2 - - + +
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Residues in contact with ARG 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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329A PRO* 3.4 8.9 + - - +
330A VAL* 1.3 69.5 - - - +
332A GLN* 1.3 76.8 + - - +
334A ASP* 3.0 31.9 + - - +
335A ARG* 3.6 3.8 + - - +
444A PHE 4.1 6.2 + - - +
446A PRO* 5.9 5.4 - - + -
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Residues in contact with GLN 332 (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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74A PHE* 3.7 23.3 - - + -
78A GLU* 5.4 1.8 - - - +
330A VAL* 3.4 0.8 - - + -
331A ARG* 1.3 82.5 + - - +
333A PHE* 1.3 63.9 + - - +
334A ASP 3.1 0.5 + - - -
335A ARG* 3.1 18.8 + - - +
336A TYR* 2.9 21.5 + - - +
443A PRO 4.2 5.3 + - - -
444A PHE* 3.5 48.4 - - + +
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Residues in contact with PHE 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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67A GLN* 3.7 43.1 - - + -
70A GLU* 3.8 4.0 - - + -
71A ALA* 3.1 40.2 - - + -
74A PHE* 3.7 16.7 - + + -
330A VAL* 3.1 24.1 + - + +
332A GLN* 1.3 78.4 - - - +
334A ASP* 1.3 53.3 + - - +
336A TYR* 3.8 22.2 - + - -
337A PHE* 2.7 55.0 + + + +
384A TYR* 3.8 6.5 - - - -
386A GLN* 3.4 20.9 - - - +
390A ILE* 4.0 9.4 - - + -
394A VAL* 5.8 0.2 - - + -
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Residues in contact with ASP 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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329A PRO* 4.8 7.4 - - - +
330A VAL 3.5 3.9 + - - +
331A ARG* 3.0 24.4 + - - +
333A PHE* 1.3 79.8 - - - +
335A ARG* 1.3 64.3 + - - +
337A PHE* 4.0 0.7 - - - +
338A GLN* 3.0 40.6 + - - +
384A TYR* 2.5 37.8 + - - -
386A GLN* 3.3 22.4 + - - +
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Residues in contact with ARG 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 ARG 3.6 3.6 + - - +
332A GLN* 3.1 19.4 + - - +
334A ASP* 1.3 78.3 - - - +
336A TYR* 1.3 63.2 + - - +
338A GLN* 4.0 8.0 - - - +
339A SER* 3.3 26.7 + - - -
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Residues in contact with TYR 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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70A GLU* 2.6 37.8 + - + -
73A LEU* 4.0 1.7 - - - +
74A PHE* 3.2 46.4 - + + -
77A ASP* 4.6 7.4 - - - -
332A GLN 2.9 13.0 + - - +
333A PHE* 3.3 23.3 - + - +
335A ARG* 1.3 76.8 - - - +
337A PHE* 1.3 65.6 + - - +
339A SER* 2.6 29.5 + - - -
340A LEU* 3.7 20.9 + - + +
347A ARG* 2.8 25.6 + - - -
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Residues in contact with PHE 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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62A GLU 5.5 1.3 - - - -
63A ASP* 5.7 0.4 - - - -
66A ILE* 4.1 13.0 - - + -
67A GLN* 3.9 21.5 - - + -
70A GLU* 4.0 21.3 - - + -
333A PHE* 2.7 36.8 + + + +
334A ASP 4.1 1.8 - - - +
336A TYR* 1.3 70.5 - - - +
338A GLN* 1.3 56.9 + - - +
339A SER 2.7 11.2 + - - -
340A LEU* 2.8 49.3 + - + +
351A PHE* 4.7 1.6 - + - -
354A PHE* 4.0 17.7 - + - -
358A LYS* 5.4 2.5 - - - -
379A ILE* 4.0 29.7 - - + +
384A TYR* 3.6 40.6 - + + +
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Residues in contact with GLN 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 ASP* 3.0 30.7 + - - +
335A ARG* 4.0 6.7 - - - +
337A PHE* 1.3 74.4 - - - +
339A SER* 1.3 57.2 + - - +
340A LEU 3.2 5.6 + - - +
378A ALA* 5.4 2.6 - - - +
379A ILE* 3.0 32.3 + - - +
380A ASP* 3.0 28.4 - - - -
381A SER* 3.1 10.9 + - - +
384A TYR* 3.3 32.0 - - + -
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Residues in contact with SER 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 ARG* 3.3 16.4 + - - -
336A TYR* 2.6 27.0 + - - -
337A PHE 2.7 1.2 + - - -
338A GLN* 1.3 77.6 - - - +
340A LEU* 1.3 63.0 + - - +
341A ASN* 4.0 1.7 - - - +
344A 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