Contacts of the helix formed by residues 59 - 70 (chain O) in PDB entry 3HOU
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 59 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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854N LEU* 4.7 14.5 - - + +
856N PHE* 5.8 2.0 - - + -
950N ASP* 5.3 1.1 - - - +
969N ARG* 3.8 30.7 - - - +
54O ASN* 4.5 0.9 - - - +
57O VAL 4.1 0.8 + - - -
58O LEU* 1.3 75.5 - - - +
60O ASP* 1.3 71.6 + - - +
61O GLU* 3.3 8.3 - - - +
62O PHE* 2.8 28.7 + - + +
63O ILE* 3.1 7.7 + - - +
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Residues in contact with ASP 60 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948N ILE* 6.2 0.7 - - - -
969N ARG* 3.3 19.2 + - - +
51O VAL* 3.4 23.0 - - + +
54O ASN* 3.3 20.3 + - - +
59O ALA* 1.3 73.8 - - - +
61O GLU* 1.3 61.6 + - - +
63O ILE* 3.1 7.6 + - - +
64O ALA* 2.8 27.6 + - - +
60X ARG* 2.9 36.0 + - - -
67X PHE* 3.5 28.4 - - + -
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Residues in contact with GLU 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797N TYR* 3.4 6.7 + - - +
852N ARG* 5.3 0.9 + - - -
854N LEU* 4.7 0.9 - - + -
904N ARG* 6.0 0.7 - - - +
948N ILE* 5.6 0.9 - - - -
969N ARG* 2.3 52.6 + - - +
970N THR* 4.2 1.2 - - - -
971N THR* 2.8 40.9 + - - +
59O ALA* 4.4 2.9 - - - -
60O ASP* 1.3 73.0 + - - +
62O PHE* 1.3 61.2 + - - +
64O ALA* 3.7 10.2 - - + +
65O HIS* 2.9 28.4 + - - +
67X PHE* 4.0 19.3 - - + -
68X GLU* 5.5 4.9 - - - +
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Residues in contact with PHE 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785N TYR* 5.7 1.8 - - - -
797N TYR* 3.9 37.0 - + + -
798N TYR* 3.1 44.9 - + - -
854N LEU* 4.9 11.7 - - + -
58O LEU* 3.7 28.5 - - + -
59O ALA* 2.8 27.9 + - + +
61O GLU* 1.3 79.6 - - + +
63O ILE* 1.3 62.0 + - - +
65O HIS* 3.2 12.0 - - - +
66O ARG* 2.9 30.4 - - - +
1V MET* 3.6 37.7 - - + -
2V ILE* 5.0 0.4 - - + -
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Residues in contact with ILE 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O VAL* 6.3 0.2 - - + -
54O ASN* 4.2 9.6 - - - +
56O THR* 4.1 9.6 - - - +
58O LEU* 3.6 30.1 - - + +
59O ALA 3.1 11.4 + - - +
60O ASP* 3.5 6.5 - - - +
62O PHE* 1.3 71.2 - - - +
64O ALA* 1.3 67.4 + - - +
65O HIS 3.0 1.3 - - - -
66O ARG* 2.9 21.8 + - - +
67O LEU* 2.9 31.2 + - + +
144O ILE* 4.5 16.6 - - + -
145O CYS* 4.6 5.8 - - + -
153O LEU* 3.9 28.0 - - + -
155O LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O VAL* 4.2 15.9 - - + +
60O ASP 2.8 17.0 + - - +
61O GLU* 3.8 11.2 - - - +
63O ILE* 1.3 77.0 - - - +
65O HIS* 1.3 65.6 + - - +
67O LEU* 3.4 21.7 + - - +
68O GLY 3.4 6.1 + - - -
67X PHE* 4.0 24.0 - - + -
68X GLU 4.4 8.3 - - - +
69X ALA* 4.1 13.2 - - - +
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Residues in contact with HIS 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797N TYR* 4.3 13.7 - + + -
798N TYR* 4.3 18.1 - + - -
847N ASP 2.8 29.7 + - - -
848N ARG 3.7 3.8 + - - -
849N GLY* 3.5 20.0 + - - -
852N ARG* 3.7 24.0 - - - +
61O GLU 2.9 14.1 + - - +
62O PHE* 3.2 12.1 - - - +
63O ILE 3.0 0.2 - - - -
64O ALA* 1.3 77.2 - - - +
66O ARG* 1.3 56.4 + - - +
68O GLY* 2.9 11.4 + - - -
69O LEU* 2.6 43.1 - - + +
167O HIS* 4.9 2.4 - + - -
68X GLU 5.7 0.2 - - - -
69X ALA 4.2 3.1 - - - +
70X ARG 3.7 21.0 - - - -
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Residues in contact with ARG 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798N TYR* 2.8 20.2 + - - +
58O LEU* 4.7 2.5 - - - -
62O PHE* 2.9 31.6 - - - +
63O ILE* 3.2 12.1 - - + +
65O HIS* 1.3 68.8 - - + +
67O LEU* 1.3 53.2 + - + +
68O GLY 2.6 17.4 + - - -
69O LEU* 2.6 27.1 + - - +
70O ILE* 3.1 15.1 + - + +
143O LEU 3.4 9.5 + - - -
144O ILE* 2.7 39.3 + - + +
2V ILE* 2.6 28.3 - - - +
3V VAL 2.3 30.1 + - - -
4V PRO* 3.7 1.8 - - - +
5V VAL* 3.0 40.5 - - + +
15V GLY* 5.7 0.6 - - - -
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Residues in contact with LEU 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O ILE* 3.4 39.7 - - + +
49O VAL* 3.8 24.2 - - + -
63O ILE* 2.9 22.2 + - + +
64O ALA* 3.5 8.5 - - - +
65O HIS 3.3 0.2 - - - -
66O ARG* 1.3 76.4 - - - +
68O GLY* 1.3 59.3 + - - +
70O ILE* 3.7 21.8 - - + +
101O LEU* 5.0 0.4 - - + -
118O LEU* 4.6 8.7 - - + -
144O ILE* 3.3 36.3 - - + -
155O LEU* 3.3 33.7 - - + -
157O CYS* 4.1 6.1 - - - -
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Residues in contact with GLY 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O ALA* 3.9 12.1 - - - +
46O ILE* 3.7 20.6 - - - +
64O ALA 3.4 3.0 + - - -
65O HIS 2.9 9.8 + - - -
66O ARG 2.6 6.9 + - - -
67O LEU* 1.3 78.6 - - - +
69O LEU* 1.3 59.8 + - - -
70O ILE 3.9 2.9 - - - +
169O LYS* 3.2 25.1 - - - +
69X ALA* 3.8 11.4 - - - -
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Residues in contact with LEU 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798N TYR* 6.4 1.3 - - + -
847N ASP 5.8 0.2 - - - -
848N ARG* 3.7 42.0 - - + +
65O HIS* 2.6 49.6 - - + +
66O ARG* 2.6 23.3 + - - +
68O GLY* 1.3 70.6 - - - -
70O ILE* 1.3 60.1 + - - +
71O PRO* 3.0 3.1 - - - +
167O HIS* 5.9 1.6 - - + -
169O LYS* 4.3 11.9 - - + -
5V VAL* 3.6 30.7 - - + +
6V ARG* 2.8 50.3 + - - +
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Residues in contact with ILE 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O ALA* 5.2 1.9 - - - +
46O ILE* 5.8 0.4 - - + -
66O ARG 3.1 10.0 + - - +
67O LEU* 3.7 26.7 - - + +
68O GLY 3.3 6.8 - - - +
69O LEU* 1.3 76.5 - - - +
71O PRO* 1.3 82.5 - - + +
72O LEU* 3.7 17.1 - - + +
115O SER* 3.7 25.8 - - - +
118O LEU* 4.4 14.6 - - + -
132O PRO* 5.2 0.4 - - + -
142O VAL* 3.8 18.4 - - + -
144O ILE* 3.4 39.9 - - + -
5V VAL* 4.1 4.0 - - + +
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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