Contacts of the helix formed by residues 333 - 347 (chain A) in PDB entry 3HEG
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 LEU 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 4.6 7.9 - - + -
332A LEU* 1.3 77.7 - - - +
334A ILE* 1.3 65.9 + - - +
335A ASP* 4.2 9.2 - - + +
336A GLU* 3.0 35.4 + - + +
337A TRP* 3.1 26.8 + - - -
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Residues in contact with ILE 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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59A PHE* 3.2 29.8 - - + +
60A GLN 4.0 7.4 - - - +
61A SER* 3.5 39.7 - - - +
62A ILE* 3.5 16.0 - - + +
65A ALA* 4.2 8.1 - - + +
333A LEU* 1.3 73.5 - - - +
335A ASP* 1.3 66.2 + - - +
337A TRP* 3.5 2.3 + - - +
338A LYS* 2.8 34.9 + - + +
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Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 5.6 0.7 - - - +
333A LEU* 3.3 7.2 - - + +
334A ILE* 1.3 85.9 - - - +
336A GLU* 1.3 60.5 + - + +
338A LYS* 3.8 17.6 + - - +
339A SER* 2.9 28.8 + - - -
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Residues in contact with GLU 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 LEU* 3.6 27.5 - - + +
333A LEU* 3.0 51.3 + - + +
335A ASP* 1.3 76.3 - - + +
337A TRP* 1.3 65.7 + - - +
338A LYS 3.1 1.1 - - - -
339A SER* 3.2 5.8 + - - -
340A LEU* 3.0 32.2 + - + +
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Residues in contact with TRP 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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59A PHE* 5.0 0.2 - - - -
62A ILE* 3.8 30.9 - - + +
65A ALA* 3.5 24.7 - - + +
66A LYS* 3.6 30.9 - - + +
69A TYR* 3.7 42.1 - + + +
327A PHE* 3.6 27.8 - + + -
330A ARG* 3.4 22.9 - - + -
332A LEU* 3.4 43.3 + - + +
333A LEU 3.1 24.2 + - - +
334A ILE 4.6 0.2 - - - -
336A GLU* 1.3 75.5 - - - +
338A LYS* 1.3 57.6 + - - +
340A LEU* 3.6 9.3 + - + +
341A THR* 3.0 32.6 + - - -
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Residues in contact with LYS 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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59A PHE* 3.8 44.2 - - + -
96A LEU* 4.6 15.4 + - + +
97A GLU 5.1 4.2 + - - -
99A PHE* 2.7 49.5 + - + +
100A ASN* 4.2 13.0 - - - +
334A ILE* 2.8 22.8 + - - +
335A ASP* 3.8 19.3 + - - +
336A GLU 3.1 0.2 - - - -
337A TRP* 1.3 75.4 - - - +
339A SER* 1.3 57.9 + - - +
341A THR* 3.4 0.9 + - - -
342A TYR* 3.0 22.9 + - - +
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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
----------------------------------------------------------
96A LEU* 3.9 30.9 - - - +
335A ASP 2.9 18.7 + - - -
336A GLU* 3.2 6.7 + - - -
338A LYS* 1.3 74.3 - - - +
340A LEU* 1.3 59.3 + - - +
342A TYR* 3.1 4.2 + - - +
343A ASP* 2.9 38.0 + - - +
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Residues in contact with LEU 340 (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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69A TYR* 3.5 27.0 - - + +
327A PHE* 6.1 0.9 - - + -
332A LEU* 3.8 27.1 - - + -
336A GLU* 3.0 19.4 + - + +
337A TRP* 3.7 18.8 - - + +
339A SER* 1.3 76.5 - - - +
341A THR* 1.3 63.3 + - - +
343A ASP* 3.6 17.1 - - + +
344A GLU* 3.1 27.5 + - - +
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Residues in contact with THR 341 (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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59A PHE* 3.8 27.9 - - + -
65A ALA 4.4 0.2 + - - -
68A THR* 4.0 11.9 - - + -
69A TYR* 3.4 31.8 + - - +
72A LEU* 3.9 17.9 - - + -
99A PHE* 4.0 7.2 - - + -
102A VAL* 4.2 4.9 - - + -
337A TRP 3.0 19.0 + - - -
338A LYS 3.6 4.7 - - - -
339A SER 3.3 0.2 - - - -
340A LEU* 1.3 71.7 - - - +
342A TYR* 1.3 60.0 + - - +
344A GLU* 3.1 6.1 + - - +
345A VAL* 2.9 33.6 + - + +
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Residues in contact with TYR 342 (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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91A THR* 4.4 11.0 - - + -
93A ALA* 4.5 4.3 + - + -
94A ARG 3.3 24.6 + - - -
95A SER* 3.5 12.3 - - - -
96A LEU* 3.6 38.4 - - + -
99A PHE* 3.5 45.5 - + + -
338A LYS 3.0 9.2 + - - +
339A SER 3.1 8.2 + - - +
341A THR* 1.3 73.4 - - - +
343A ASP* 1.3 71.8 + - - +
345A VAL* 3.1 6.0 + - + +
346A ILE* 3.0 50.2 + - + +
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Residues in contact with ASP 343 (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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339A SER* 2.9 28.3 + - - +
340A LEU* 3.6 23.2 - - - +
342A TYR* 1.3 80.9 - - - +
344A GLU* 1.3 60.1 + - + +
346A ILE* 2.9 9.9 + - - +
347A SER* 2.8 34.1 + - - -
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Residues in contact with GLU 344 (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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69A TYR* 3.7 21.5 + - + -
72A LEU* 3.6 19.3 - - + -
73A ARG* 3.3 28.7 + - + -
76A LYS* 2.5 61.6 + - + +
340A LEU 3.1 13.8 + - - +
341A THR* 3.1 9.9 + - - +
343A ASP* 1.3 81.4 - - + +
345A VAL* 1.3 60.6 + - - +
347A SER* 3.5 6.9 + - - -
348A PHE* 3.5 6.1 + - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.7 15.5 - - + -
89A VAL* 4.1 34.4 - - + +
90A PHE 5.8 0.7 - - - -
91A THR* 4.0 29.4 - - + +
99A PHE* 4.3 16.2 - - + -
102A VAL* 4.9 4.3 - - + -
341A THR* 2.9 22.8 + - + +
342A TYR* 3.1 9.2 + - + +
344A GLU* 1.3 79.7 - - - +
346A ILE* 1.3 68.3 + - + +
348A PHE* 3.6 14.7 + - - +
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Residues in contact with ILE 346 (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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91A THR* 5.5 2.5 - - + -
342A TYR* 3.0 47.2 + - + +
343A ASP* 2.9 11.0 + - - +
345A VAL* 1.3 90.3 - - + +
347A SER* 1.3 59.8 + - - +
348A PHE 3.2 8.4 + - - +
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Residues in contact with SER 347 (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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76A LYS* 3.0 23.5 + - - -
343A ASP* 2.8 16.6 + - - -
344A GLU* 3.6 5.9 + - - -
346A ILE* 1.3 77.1 - - - +
348A PHE* 1.3 62.4 + - - +
349A VAL* 3.5 12.6 + - - +
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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