Contacts of the helix formed by residues 105 - 115 (chain X) in PDB entry 4HSC
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 HIS 105 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103X GLU* 3.0 41.0 + - + +
104X ASP* 1.3 77.2 + - - +
106X THR* 1.3 64.3 + - - +
107X GLU 3.4 2.0 - - - -
108X GLU* 3.0 31.0 + - + +
109X ILE* 2.9 23.9 + - + +
318X LYS 3.1 18.5 + - - -
319X SER* 4.1 8.2 + - - -
320X VAL 3.2 23.1 - - - +
321X THR* 3.4 23.8 - - + +
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Residues in contact with THR 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X ASP* 2.6 33.1 + - - -
105X HIS* 1.3 71.6 - - - +
107X GLU* 1.3 69.3 + - + +
109X ILE* 3.1 11.9 + - - +
110X ASN* 3.1 21.9 + - - +
313X ALA* 3.7 25.0 + - + +
314X ASP* 5.7 2.5 - - - +
316X PHE 5.8 0.2 + - - -
318X LYS* 4.5 11.1 + - - +
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Residues in contact with GLU 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X ASP* 4.6 2.3 + - - +
105X HIS 3.4 0.6 - - - -
106X THR* 1.3 80.6 - - + +
108X GLU* 1.3 58.2 + - - +
110X ASN* 3.8 6.1 - - - +
111X ASP* 2.9 44.5 + - - +
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Residues in contact with GLU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X HIS* 3.0 36.7 + - + +
107X GLU* 1.3 79.4 - - - +
109X ILE* 1.3 63.4 + - - +
111X ASP* 3.3 3.6 + - - +
112X LYS* 2.9 34.1 + - + +
321X THR* 4.2 4.8 - - - -
322X PHE* 3.2 36.2 + - + +
323X LYS* 4.2 6.1 + - - +
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Residues in contact with ILE 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X HIS 2.9 19.2 + - - +
106X THR* 3.6 6.5 - - - +
108X GLU* 1.3 75.8 - - + +
110X ASN* 1.3 59.2 + - - +
112X LYS* 3.8 2.9 - - - +
113X ILE* 2.8 56.3 + - + +
313X ALA* 4.0 13.5 - - + +
316X PHE* 3.7 27.6 - - + -
320X VAL* 3.7 16.8 - - + +
321X THR* 3.4 9.6 - - - +
322X PHE* 3.2 36.3 - - + +
325X LEU* 4.2 9.9 - - + -
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Residues in contact with ASN 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X THR* 3.1 19.9 + - - +
107X GLU* 3.8 6.1 - - - +
109X ILE* 1.3 79.7 - - - +
111X ASP* 1.3 59.7 + - - +
113X ILE* 3.8 3.6 - - - +
114X TYR* 2.8 50.0 + - + -
311X ASN* 3.8 23.0 + - - +
312X PRO* 3.5 10.9 - - - +
313X ALA* 2.7 43.6 + - - +
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Residues in contact with ASP 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X GLU* 2.9 35.3 + - - +
108X GLU* 4.0 4.0 - - - +
110X ASN* 1.3 76.6 - - - +
112X LYS* 1.3 55.1 - - + +
114X TYR* 3.6 11.5 + - - +
115X SER* 2.7 37.0 + - - +
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Residues in contact with LYS 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X GLU* 2.9 27.4 + - + +
109X ILE 4.0 0.2 - - - +
111X ASP* 1.3 75.9 - - + +
113X ILE* 1.3 65.0 + - - +
115X SER* 3.3 16.6 + - - +
116X LEU* 3.4 18.4 + - - +
322X PHE* 3.5 52.1 - - + +
326X GLN* 5.7 0.4 + - - -
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Residues in contact with ILE 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X ILE* 2.8 37.4 + - + +
110X ASN 4.0 1.6 - - - +
112X LYS* 1.3 74.2 - - - +
114X TYR* 1.3 65.2 + - - +
116X LEU* 3.1 32.1 + - + +
312X PRO* 3.6 27.4 - - + -
316X PHE* 4.1 5.2 - - + -
322X PHE* 4.6 12.8 - - + -
325X LEU* 4.3 7.4 - - + -
330X VAL* 5.8 0.4 - - + -
336X PRO* 4.5 11.7 - - + -
438X LEU* 4.0 17.5 - - + -
439X LYS* 3.6 38.6 - - + +
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Residues in contact with TYR 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X ASN* 2.8 43.1 + - + +
111X ASP* 4.0 12.1 - - - +
113X ILE* 1.3 73.2 - - - +
115X SER* 1.3 60.3 + - - +
116X LEU 3.7 0.2 - - - +
311X ASN* 2.9 31.2 + - - -
312X PRO* 3.3 29.7 - - + +
439X LYS* 3.4 44.8 + - + +
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Residues in contact with SER 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X ASP* 2.7 22.8 + - - +
112X LYS* 3.6 14.9 - - - +
113X ILE 3.1 0.6 - - - -
114X TYR* 1.3 75.4 - - - +
116X LEU* 1.3 67.4 + - - +
117X ASN* 3.2 7.4 + - - +
332X ASN* 4.6 0.7 + - - -
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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