Contacts of the helix formed by residues 138 - 151 (chain P) 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 ASN 138 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134P THR* 3.5 30.8 - - + +
135P GLY* 3.9 9.3 - - - +
137P ASN* 1.3 75.2 + - - +
139P LYS* 1.3 52.5 + - - +
140P ASP* 2.5 20.1 + - - +
141P LEU* 2.6 34.4 + - + +
142P LYS* 3.0 15.1 + - - +
35S GLU* 3.3 34.3 + - - +
36S GLY* 2.8 37.1 + - - -
46S LEU* 4.0 2.1 - - - +
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Residues in contact with LYS 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P ASN 2.7 20.6 + - - +
138P ASN* 1.3 71.4 - - - +
140P ASP* 1.3 76.9 + - - +
142P LYS* 3.1 16.3 + - + +
143P ASN* 2.5 45.2 + - - +
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Residues in contact with ASP 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P ASN 5.5 0.3 - - - +
138P ASN* 2.5 7.2 + - - +
139P LYS* 1.3 93.9 - - - +
141P LEU* 1.3 54.8 + - - +
142P LYS 3.0 1.9 + - - -
143P ASN* 3.1 1.9 + - - +
144P THR* 2.5 42.9 + - - -
36S GLY* 3.0 33.1 - - - +
44S TYR* 3.7 22.7 - - + -
46S LEU* 3.4 19.1 - - + -
105S PRO* 3.6 19.4 - - + +
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Residues in contact with LEU 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P ILE* 3.4 32.3 - - + -
63P LEU* 4.6 2.9 - - + -
130P LEU* 3.7 11.2 - - + -
134P THR* 3.3 35.0 - - + +
138P ASN* 2.6 30.4 + - + +
140P ASP* 1.3 73.9 - - - +
142P LYS* 1.3 56.0 + - - +
144P THR* 3.8 6.1 - - - -
145P MET* 2.8 37.8 + - - +
35S GLU* 4.5 4.9 - - - +
46S LEU* 3.8 26.1 - - + +
47S CYS* 4.1 17.5 - - + -
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Residues in contact with LYS 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P ASP* 5.7 0.7 - - - +
130P LEU* 3.4 31.3 - - + +
131P GLU* 6.1 3.0 - - - +
134P THR* 3.9 10.3 - - - +
136P GLY* 3.2 41.3 + - - +
137P ASN 3.7 0.4 - - - -
138P ASN* 3.1 31.2 - - + +
139P LYS* 3.1 17.7 - - - +
140P ASP 3.0 0.4 - - - -
141P LEU* 1.3 74.2 - - - +
143P ASN* 1.3 64.8 + - - +
144P THR 3.0 1.1 - - - -
145P MET* 2.7 20.8 + - - +
146P GLN* 3.0 17.6 + - - +
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Residues in contact with ASN 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P LYS* 2.5 35.5 + - - +
140P ASP* 3.8 2.9 - - - +
142P LYS* 1.3 83.1 - - - +
144P THR* 1.3 56.3 + - - +
146P GLN* 3.9 16.6 - - - +
147P TYR* 3.0 32.4 + - - +
102S GLN* 3.6 29.0 + - - +
104S GLY 4.3 7.5 - - - +
105S PRO* 4.6 4.7 - - + -
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Residues in contact with THR 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ILE* 4.5 8.5 - - + -
140P ASP 2.5 29.4 + - - -
141P LEU* 3.8 7.9 - - - -
143P ASN* 1.3 73.3 - - - +
145P MET* 1.3 52.8 + - - +
147P TYR* 4.2 3.5 - - - +
148P LEU* 2.8 48.5 + - + +
2S PHE* 3.5 26.2 - - + -
46S LEU* 3.2 36.0 - - + +
104S GLY* 4.7 0.2 - - - -
105S PRO* 3.2 15.8 - - + +
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Residues in contact with MET 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P ARG* 4.4 15.0 - - + +
59P ILE* 3.2 46.7 - - + -
60P LYS* 4.6 5.2 - - + -
63P LEU* 5.3 2.5 - - + -
123P LEU* 5.4 0.4 - - - -
126P ILE* 3.3 54.9 - - + +
130P LEU* 4.0 17.3 - - + -
141P LEU* 2.8 19.4 + - + +
142P LYS* 2.7 12.8 + - - +
144P THR* 1.3 77.5 - - - +
146P GLN* 1.3 57.8 + - + +
148P LEU* 3.9 4.2 - - - +
149P THR* 2.8 30.5 + - - -
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Residues in contact with GLN 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P LEU* 3.7 18.9 - - + +
127P ASP* 5.6 6.9 + - - -
142P LYS 3.0 14.4 + - - +
143P ASN* 3.9 17.4 - - - +
145P MET* 1.3 74.6 - - + +
147P TYR* 1.3 71.3 + - - +
148P LEU 3.0 0.7 - - - -
149P THR* 2.6 30.9 + - - +
150P ASN* 2.8 17.0 + - - +
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Residues in contact with TYR 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P LEU* 3.3 33.2 - - + +
143P ASN 3.0 16.3 + - - +
144P THR 4.2 0.9 - - - +
146P GLN* 1.3 80.9 - - - +
148P LEU* 1.3 64.8 + - - +
150P ASN* 4.6 0.2 - - - +
151P PHE* 2.9 53.3 + + - +
2S PHE* 4.7 13.0 - + - -
79S PHE* 6.0 0.7 - + - -
87S VAL* 5.1 0.5 - - - +
88S ASP* 2.3 37.6 + - - -
89S GLY* 3.5 15.0 - - - -
90S THR* 6.0 0.4 - - - -
102S GLN* 3.7 9.0 - - - +
103S VAL* 3.1 20.0 - - + +
104S GLY* 3.2 35.9 - - - +
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Residues in contact with LEU 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 3.8 23.1 - - + -
53P SER 3.3 29.4 - - - +
55P ALA* 3.7 13.5 - - + +
56P ARG* 3.1 38.1 - - + +
59P ILE* 4.5 12.1 - - + -
144P THR* 2.8 35.8 + - + +
145P MET* 3.9 6.5 - - - +
146P GLN 2.8 2.6 + - - -
147P TYR* 1.3 74.7 - - - +
149P THR* 1.3 57.9 + - - +
151P PHE 3.9 0.3 - - - -
152P SER* 2.7 35.5 + - - -
2S PHE* 4.3 12.8 - - + -
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Residues in contact with THR 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P ARG* 3.4 18.5 + - - +
119P ARG* 4.0 2.8 + - - -
122P GLU* 3.1 26.3 + - - +
123P LEU* 3.1 39.6 + - + +
126P ILE* 4.7 3.4 - - - -
145P MET 2.8 18.2 + - - +
146P GLN* 2.6 30.4 + - - +
148P LEU* 1.3 73.2 - - - +
150P ASN* 1.3 65.4 + - - +
152P SER* 3.9 6.9 - - - -
155P ARG* 4.6 3.3 - - - -
221P TYR* 2.9 18.0 + - - -
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Residues in contact with ASN 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P ARG* 4.7 9.9 + - - +
123P LEU* 3.7 18.3 - - - +
146P GLN* 2.8 41.0 + - - +
147P TYR 4.2 0.4 - - - +
149P THR* 1.3 81.2 - - - +
151P PHE* 1.3 80.5 + - + +
152P SER 3.1 10.3 + - - +
221P TYR* 3.3 23.7 + - - -
142S ARG* 3.7 28.0 + - - +
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Residues in contact with PHE 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52P LEU* 4.0 24.6 - - + +
147P TYR* 2.9 42.3 + + + +
148P LEU 3.9 2.5 - - - -
150P ASN* 1.3 94.2 - - + +
152P SER* 1.3 60.7 + - - +
153P ARG* 3.5 4.5 + - - +
182P SER* 5.1 5.5 - - - +
88S ASP* 3.8 26.9 - - - +
89S GLY* 3.8 20.6 - - - -
90S THR* 3.1 29.8 - - - -
142S ARG* 3.6 35.0 - - + +
171S ILE* 5.7 0.4 - - + -
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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