Contacts of the helix formed by residues 101 - 113 (chain P) in PDB entry 4UJ3
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 101 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19P ASP* 2.9 38.7 + - - +
97P LEU* 3.3 32.6 + - - +
98P THR 4.1 2.9 - - - +
99P TYR 3.1 0.8 - - - -
100P GLU* 1.3 74.1 - - - +
102P VAL* 1.3 64.8 + - - +
103P GLU 3.1 3.4 - - - -
104P ARG* 2.9 55.0 + - + +
105P TRP* 3.0 18.1 + - + +
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Residues in contact with VAL 102 (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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89P LEU* 3.7 31.4 - - + -
90P VAL 5.4 0.2 - - - +
91P TYR* 4.3 8.3 - - + -
98P THR 3.9 11.8 + - - +
99P TYR* 3.0 31.2 + - + +
101P ASN* 1.3 77.6 - - - +
103P GLU* 1.3 52.1 + - - +
105P TRP* 3.1 8.0 + - + +
106P LEU* 2.7 34.6 + - + +
121P LEU* 3.7 18.6 - - + -
142P PHE* 3.7 29.6 - - + -
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Residues in contact with GLU 103 (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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100P GLU 3.7 10.5 + - - +
101P ASN 3.1 0.4 - - - -
102P VAL* 1.3 80.9 - - - +
104P ARG* 1.3 57.1 + - + +
106P LEU* 3.3 7.9 + - - +
107P LYS* 2.8 28.5 + - - +
142P PHE* 4.8 14.6 - - + -
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Residues in contact with ARG 104 (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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101P ASN* 2.9 43.2 + - + +
103P GLU* 1.3 79.5 - - + +
105P TRP* 1.3 60.2 + - + +
107P LYS* 3.2 9.9 - - - +
108P GLU* 3.1 29.6 + - - +
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Residues in contact with TRP 105 (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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17P ILE* 3.9 20.0 - - + +
18P GLY* 3.4 41.5 - - - -
19P ASP* 2.6 32.5 + - - +
69P GLY* 3.2 25.4 - - - -
71P GLU* 4.7 16.2 - - + -
81P TYR* 4.3 7.4 - - - -
89P LEU* 3.7 24.0 - - + -
90P VAL 5.5 0.7 - - - -
98P THR 5.2 2.7 - - - -
101P ASN* 3.0 29.5 + - + +
102P VAL* 3.6 7.9 - - - +
104P ARG* 1.3 77.7 - - + +
106P LEU* 1.3 64.9 + - - +
107P LYS 3.1 1.3 - - - -
108P GLU* 3.5 29.0 + - + +
109P LEU* 3.2 21.8 + - - +
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P LEU* 3.6 19.3 - - + +
102P VAL* 2.7 15.8 + - + +
103P GLU* 3.6 7.2 - - - +
105P TRP* 1.3 73.0 - - - +
107P LYS* 1.3 61.4 + - - +
109P LEU* 3.4 5.0 + - + +
110P ARG* 3.1 23.9 + - - +
119P ILE* 3.7 31.0 - - + -
142P PHE* 4.0 22.7 - - + -
146P ASN* 4.3 11.9 - - + +
148P LEU* 3.6 38.8 - - + -
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Residues in contact with LYS 107 (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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103P GLU 2.8 14.7 + - - +
104P ARG* 3.2 15.7 - - - +
105P TRP 3.1 0.2 - - - -
106P LEU* 1.3 73.8 - - - +
108P GLU* 1.3 66.0 + - + +
110P ARG* 3.1 14.2 + - - +
111P ASP* 3.2 24.0 + - - +
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Residues in contact with GLU 108 (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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71P GLU* 3.6 29.4 - - - +
77P THR* 4.8 5.6 - - - +
81P TYR* 3.1 30.6 + - + +
104P ARG 3.1 12.7 + - - +
105P TRP* 3.5 19.8 + - + +
107P LYS* 1.3 78.2 - - + +
109P LEU* 1.3 58.3 + - - +
111P ASP* 4.3 6.3 - - - -
112P HIS* 2.9 47.6 + - + +
113P ALA 4.0 0.9 + - - -
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Residues in contact with LEU 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ILE* 3.8 24.7 - - + -
81P TYR* 3.6 31.6 - - + -
87P ALA* 4.0 16.6 - - + -
89P LEU* 4.8 0.7 - - + -
105P TRP 3.2 7.9 + - - +
106P LEU* 3.4 16.6 - - + +
107P LYS 3.1 0.2 - - - -
108P GLU* 1.3 80.0 - - - +
110P ARG* 1.3 60.1 + - - +
111P ASP 3.3 1.0 + - - -
113P ALA* 3.1 33.5 + - + +
114P ASP 4.4 3.1 - - - +
117P ILE* 4.7 9.1 - - + +
119P ILE* 3.1 52.3 - - + -
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Residues in contact with ARG 110 (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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106P LEU 3.1 14.3 + - - +
107P LYS* 3.1 7.2 + - - +
109P LEU* 1.3 75.2 - - - +
111P ASP* 1.3 66.2 + - - +
113P ALA 4.6 1.9 - - - +
115P SER* 6.4 1.6 - - - +
103V GLU* 6.5 0.9 - - + -
142V PHE* 5.9 2.6 - - - -
145V LYS* 3.9 13.2 + - - +
146V ASN* 5.2 3.6 + - - -
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Residues in contact with ASP 111 (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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107P LYS* 3.4 19.5 - - - +
108P GLU* 3.1 3.4 + - - +
110P ARG* 1.3 85.6 - - - +
112P HIS* 1.3 80.7 + - + +
113P ALA 3.4 0.2 - - - -
142V PHE* 5.8 5.0 - - - -
145V LYS* 2.2 38.9 + - - +
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Residues in contact with HIS 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P THR* 3.2 28.4 + - + +
78P SER* 4.5 16.4 - - - +
81P TYR* 3.7 29.8 - + + +
82P ARG* 5.1 0.7 + - - -
108P GLU* 2.9 30.1 + - + +
111P ASP* 1.3 94.8 - - + +
113P ALA* 1.3 59.2 + - - +
145V LYS* 4.1 1.8 - - - -
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Residues in contact with ALA 113 (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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81P TYR* 3.5 34.3 - - + +
108P GLU 4.0 0.4 + - - -
109P LEU* 3.1 28.8 + - + +
110P ARG 4.6 2.1 - - - +
111P ASP 3.4 0.2 - - - -
112P HIS* 1.3 81.3 - - - +
114P ASP* 1.3 70.2 + - - +
115P SER* 3.5 1.4 + - - -
117P ILE* 4.5 10.1 - - + -
145V LYS* 3.1 19.2 + - - -
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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