Contacts of the helix formed by residues 101 - 114 (chain D) in PDB entry 4U2M
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 MET 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D CYS 4.2 12.3 - - - +
46D SER* 4.2 12.8 - - - +
73D VAL* 3.9 14.6 - - + -
76D PHE* 3.9 20.0 - - + -
77D MET* 3.6 34.1 - - + -
96D ALA* 2.8 15.5 + - + +
99D LEU* 3.8 21.5 - - + +
100D GLN* 1.3 72.5 - - - +
102D GLN* 1.3 60.7 + - - +
103D ASP* 3.4 3.4 - - + -
104D ILE* 3.2 33.4 + - + +
105D ILE* 3.0 28.8 + - - +
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Residues in contact with GLN 102 (chain D).
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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100D GLN 3.4 6.9 + - - +
101D MET* 1.3 70.1 - - - +
103D ASP* 1.3 63.0 + - - +
105D ILE* 3.2 29.4 + - + +
106D THR* 2.9 48.3 + - - +
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Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PHE* 4.8 12.7 - - + -
101D MET* 5.1 1.1 - - + -
102D GLN* 1.3 78.7 - - - +
104D ILE* 1.3 67.9 + - + +
106D THR* 3.9 5.0 - - - -
107D ALA* 3.0 22.9 + - - +
134D PHE* 4.3 33.6 - - + -
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 4.1 21.8 - - + -
76D PHE* 3.6 30.5 - - + -
82D LEU* 4.1 20.6 - - + -
92D VAL* 3.5 26.7 - - + -
96D ALA* 3.5 18.4 - - + -
101D MET* 3.2 41.3 + - + +
103D ASP* 1.3 75.0 - - + +
105D ILE* 1.3 65.3 + - - +
107D ALA* 3.2 2.3 + - - +
108D CYS* 3.0 22.9 + - - -
134D PHE* 5.9 0.4 - - + -
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 4.0 13.2 - - + +
96D ALA* 3.8 29.6 - - + +
97D THR* 4.0 18.8 - - + +
100D GLN* 4.7 4.3 - - - -
101D MET 3.0 23.1 + - - +
102D GLN* 3.2 35.0 + - - +
104D ILE* 1.3 76.4 - - - +
106D THR* 1.3 64.1 + - - +
108D CYS* 3.3 3.3 + - - +
109D HIS* 3.0 46.9 + - + +
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Residues in contact with THR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLN* 2.9 29.7 + - - -
103D ASP* 3.9 4.7 - - - -
105D ILE* 1.3 76.9 - - - +
107D ALA* 1.3 59.6 + - - +
109D HIS* 3.2 8.3 + - + +
110D ALA* 2.8 31.4 + - + +
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Residues in contact with ALA 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LEU* 3.7 17.5 - - + -
84D LEU* 3.8 4.2 - - + +
103D ASP 3.0 17.9 + - - +
104D ILE 3.2 4.9 + - - +
106D THR* 1.3 75.5 - - - +
108D CYS* 1.3 58.3 + - - +
110D ALA* 3.2 8.5 + - - +
111D LEU* 2.9 28.9 + - - +
132D ILE* 3.6 28.8 - - + +
134D PHE* 4.7 7.9 - - + -
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Residues in contact with CYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 4.1 11.9 - - - -
89D VAL* 3.7 24.1 - - + +
92D VAL* 3.7 30.1 - - - -
93D LEU* 3.7 31.9 - - + -
104D ILE* 3.0 19.7 + - - -
105D ILE 3.6 7.9 - - - +
107D ALA* 1.3 76.5 - - - +
109D HIS* 1.3 62.2 + - - +
111D LEU* 3.2 3.6 + - - +
112D LYS* 3.0 29.2 + - - +
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Residues in contact with HIS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 3.9 27.4 - - + +
105D ILE* 3.0 40.1 + - + +
106D THR* 3.7 9.4 - - + +
108D CYS* 1.3 76.2 - - - +
110D ALA* 1.3 57.6 + - - +
112D LYS* 3.2 11.7 + - + +
113D SER* 2.8 30.4 + - - -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D THR* 2.8 24.2 + - + +
107D ALA* 3.4 9.0 - - - +
109D HIS* 1.3 74.0 - - - +
111D LEU* 1.3 63.5 + - - +
113D SER* 2.7 26.1 + - - -
114D LEU* 3.5 8.4 + - - +
132D ILE* 6.2 1.3 - - + -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.8 24.5 - - + -
85D SER 4.2 4.3 - - - +
86D PRO* 4.6 1.3 - - + -
89D VAL* 3.2 32.5 - - + -
107D ALA 2.9 13.9 + - - +
108D CYS* 3.6 7.4 - - - +
110D ALA* 1.3 76.7 - - - +
112D LYS* 1.3 63.7 + - - +
114D LEU* 3.0 39.6 + - + +
115D ALA 4.3 0.9 + - - -
126D GLY* 6.1 0.7 - - - -
128D ALA* 3.6 31.4 - - + +
130D SER* 3.9 24.7 - - - -
132D ILE* 6.2 0.2 - - + -
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Residues in contact with LYS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D VAL* 4.0 24.7 - - + -
90D ASP* 2.9 30.9 + - - -
93D LEU* 4.5 11.2 - - + +
108D CYS 3.0 20.3 + - - +
109D HIS* 3.7 15.5 - - + +
111D LEU* 1.3 76.4 - - - +
113D SER* 1.3 61.9 + - - +
114D LEU 3.0 1.8 + - - -
115D ALA* 3.1 22.4 + - - +
126D GLY* 5.7 7.2 - - - +
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D HIS 2.8 17.3 + - - -
110D ALA* 2.7 21.9 + - - +
111D LEU 3.2 0.6 - - - -
112D LYS* 1.3 71.8 - - - +
114D LEU* 1.3 63.8 + - - +
115D ALA 3.2 6.6 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA 4.1 7.4 - - - +
111D LEU* 3.0 34.9 + - + +
112D LYS 3.0 1.0 - - - -
113D SER* 1.3 84.1 + - - +
115D ALA* 1.3 59.7 + - - +
128D ALA* 4.2 19.3 - - + -
130D SER* 6.1 1.1 - - - -
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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