Contacts of the helix formed by residues 116 - 127 (chain R) 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 ASP 116 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495M GLU* 5.1 0.2 - - - +
498M ARG* 5.5 5.0 + - - -
114R GLU* 4.1 2.6 + - - +
115R THR* 1.3 81.0 + - - +
117R PRO* 1.3 68.2 - - - +
118R LEU* 2.6 38.8 + - - +
119R ARG* 3.0 31.0 + - + +
120R ILE* 2.8 29.7 + - - +
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Residues in contact with PRO 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378M GLU* 5.7 4.5 - - - +
383M TYR* 5.2 4.7 - - + -
384M ASN* 6.0 4.3 - - - +
495M GLU* 3.6 24.7 - - - +
98R ALA* 3.5 25.7 - - - +
101R ILE* 3.8 23.6 - - + +
102R SER* 4.2 12.3 - - - -
115R THR 3.9 5.6 - - - +
116R ASP* 1.3 87.8 - - - +
118R LEU* 1.3 63.7 + - - +
120R ILE* 3.3 3.8 + - + +
121R ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495M GLU* 4.4 11.2 - - - +
498M ARG* 6.0 5.4 - - - -
499M ALA* 4.8 13.0 - - + -
502M SER* 4.2 21.1 - - - +
503M GLN* 4.9 7.2 - - + +
94R LEU* 4.1 30.7 - - + +
98R ALA* 3.8 9.5 - - + +
116R ASP* 2.6 16.0 + - - +
117R PRO* 1.3 75.7 - - - +
119R ARG* 1.3 59.0 + - - +
121R ALA* 3.1 1.8 + - - +
122R MET* 2.8 55.4 + - + +
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Residues in contact with ARG 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114R GLU* 3.1 44.0 + - - +
116R ASP* 3.0 28.1 + - + +
118R LEU* 1.3 82.1 - - - +
120R ILE* 1.3 56.4 + - - +
122R MET* 3.2 25.9 + - + +
123R LYS* 2.9 28.8 + - - +
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Residues in contact with ILE 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383M TYR* 3.6 35.7 - - + -
101R ILE* 3.2 25.4 - - + -
107R VAL* 3.4 27.8 - - + -
109R VAL* 6.0 1.3 - - + -
111R LEU* 3.8 22.2 - - + -
114R GLU* 4.1 24.9 - - + +
115R THR 4.2 0.7 - - - -
116R ASP 2.8 23.7 + - - +
117R PRO 3.6 0.9 - - - +
119R ARG* 1.3 75.1 - - - +
121R ALA* 1.3 56.1 + - - +
123R LYS* 3.3 7.6 + - - +
124R GLU* 2.8 33.1 + - - +
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Residues in contact with ALA 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94R LEU* 3.5 31.9 - - + +
97R ARG* 3.8 17.0 - - + -
98R ALA* 3.8 3.6 - - - +
101R ILE* 3.7 6.5 - - + +
117R PRO 2.9 12.9 + - - +
118R LEU* 3.1 10.1 + - - +
120R ILE* 1.3 74.6 - - - +
122R MET* 1.3 60.5 + - - +
123R LYS 3.0 1.6 - - - -
124R GLU* 3.0 7.9 + - - +
125R LEU* 2.9 30.7 + - - +
130R ILE* 4.0 1.9 - - - +
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Residues in contact with MET 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503M GLN* 4.9 5.6 - - - -
90R ARG* 4.8 9.0 - - - -
94R LEU* 3.4 27.1 - - + +
118R LEU* 2.8 46.9 + - + +
119R ARG* 3.2 26.2 + - + +
121R ALA* 1.3 72.5 - - - +
123R LYS* 1.3 56.4 + - - +
125R LEU* 3.5 3.2 + - - +
126R ALA* 3.1 27.2 + - - +
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Residues in contact with LYS 123 (chain R).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109R VAL* 3.3 13.5 - - + +
110R ASP* 2.8 25.8 - - - +
111R LEU* 4.6 1.6 - - - +
112R GLU* 3.4 32.5 + - + +
114R GLU* 4.7 17.3 - - + -
119R ARG 2.9 16.0 + - - +
120R ILE* 3.5 8.7 - - + +
121R ALA 3.0 0.2 - - - -
122R MET* 1.3 76.5 - - - +
124R GLU* 1.3 64.1 + - - +
126R ALA* 3.1 16.1 + - + +
127R GLU* 2.6 46.2 + - - +
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Residues in contact with GLU 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97R ARG* 2.8 47.6 + - - +
101R ILE* 3.5 12.5 - - - +
107R VAL* 3.6 8.2 - - + -
108R PHE* 2.7 39.5 + - - -
109R VAL* 3.7 21.3 - - + -
120R ILE 2.8 20.1 + - - +
121R ALA 3.0 3.1 + - - +
123R LYS* 1.3 75.0 - - - +
125R LEU* 1.3 61.0 + - - +
127R GLU 3.3 1.9 + - - -
128R LYS 3.2 3.1 + - - -
129R LYS 2.9 34.7 + - - +
130R ILE* 3.5 13.5 - - + -
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Residues in contact with LEU 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85R MET* 4.4 24.9 - - + -
90R ARG* 4.5 24.2 - - + +
93R ILE* 4.7 4.7 - - + -
94R LEU* 4.0 32.5 - - + -
121R ALA 2.9 15.9 + - - +
122R MET* 3.8 5.4 - - - +
124R GLU* 1.3 77.1 - - - +
126R ALA* 1.3 63.0 + - - +
128R LYS* 3.3 27.6 + - + +
130R ILE* 3.6 19.5 - - + +
148R VAL* 4.4 11.9 - - + -
153R VAL* 4.8 10.9 - - + +
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Residues in contact with ALA 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122R MET 3.1 17.6 + - - +
123R LYS* 3.1 9.3 + - + +
125R LEU* 1.3 78.2 - - - +
127R GLU* 1.3 62.9 + - + +
128R LYS* 3.2 5.2 + - - +
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Residues in contact with GLU 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109R VAL* 3.4 27.2 - - + +
123R LYS* 2.6 45.0 + - - +
124R GLU 3.3 2.2 + - - +
125R LEU 3.2 0.2 - - - -
126R ALA* 1.3 81.8 - - + +
128R LYS* 1.3 69.7 + - - +
129R LYS* 2.7 36.2 + - + +
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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