Contacts of the helix formed by residues 105 - 120 (chain l) in PDB entry 5M32
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 GLN 105 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65l GLU* 5.6 11.7 - - + +
100l GLU* 6.2 1.3 - - + -
102l ALA* 3.3 20.9 + - + +
103l THR 3.2 1.8 - - - -
104l GLY* 1.3 76.9 - - - +
106l GLU* 1.3 61.3 + - + +
107l VAL 2.9 11.0 + - - -
108l GLU* 3.1 16.1 + - - +
109l LEU* 3.4 9.2 + - + +
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Residues in contact with GLU 106 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96l PHE* 4.2 21.8 - - + +
97l LEU* 5.7 0.4 - - - -
100l GLU* 4.9 11.9 - - + -
102l ALA 4.5 0.8 + - - +
103l THR 4.2 5.4 + - - +
104l GLY 3.7 0.4 - - - -
105l GLN* 1.3 76.0 - - + +
107l VAL* 1.3 63.2 + - - +
108l GLU 3.3 0.2 - - - -
109l LEU* 3.7 15.2 - - + +
110l CYS* 3.2 15.8 + - - +
136l LEU* 3.3 30.4 - - + +
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Residues in contact with VAL 107 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103l THR 4.9 2.3 + - - +
104l GLY 4.2 12.5 + - - +
105l GLN 2.9 0.4 + - - -
106l GLU* 1.3 78.9 - - - +
108l GLU* 1.3 57.5 + - + +
110l CYS* 3.8 1.9 + - - +
111l LEU* 3.2 24.7 + - - +
133l LEU* 5.1 2.1 - - - +
136l LEU* 3.8 18.6 - - + +
137l TYR* 4.5 22.3 + - + +
140l THR* 6.3 0.2 - - + -
142l ARG* 5.0 13.2 - - - +
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Residues in contact with GLU 108 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104l GLY 4.8 1.5 + - - +
105l GLN 3.1 8.5 + - - +
107l VAL* 1.3 77.1 - - + +
109l LEU* 1.3 61.6 + - - +
110l CYS 3.2 0.7 - - - -
111l LEU* 3.6 9.4 - - + +
112l GLU* 3.0 29.6 + - - +
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Residues in contact with LEU 109 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65l GLU* 6.2 4.5 - - + -
93l LEU* 5.8 2.1 - - - +
96l PHE* 4.8 15.3 - - + -
105l GLN* 3.4 7.7 + - + +
106l GLU* 3.7 21.1 - - + -
107l VAL 3.4 0.8 - - - -
108l GLU* 1.3 79.4 - - - +
110l CYS* 1.3 58.1 + - - +
112l GLU* 4.0 5.3 + - - +
113l CYS* 3.8 14.7 + - - +
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Residues in contact with CYS 110 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93l LEU* 6.0 3.1 - - + -
96l PHE* 6.5 0.4 - - + -
106l GLU 3.2 17.2 + - - +
107l VAL 4.4 1.1 - - - +
109l LEU* 1.3 75.4 - - - +
111l LEU* 1.3 60.6 + - - +
112l GLU 3.3 0.4 - - - -
113l CYS* 3.2 10.7 + - + +
114l ILE* 2.9 31.1 + - - +
129l LEU* 5.1 13.8 - - + +
132l ARG 6.3 0.2 - - - -
133l LEU* 4.2 17.3 - - + -
136l LEU* 4.0 16.6 - - + -
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Residues in contact with LEU 111 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107l VAL 3.2 20.0 + - - +
108l GLU* 3.4 10.9 + - + -
110l CYS* 1.3 75.6 - - - +
112l GLU* 1.3 58.7 + - - +
114l ILE* 3.1 10.3 + - - +
115l GLU* 3.0 31.6 + - - +
133l LEU* 4.5 6.0 - - + +
137l TYR* 5.3 4.7 - - - +
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Residues in contact with GLU 112 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108l GLU 3.0 17.8 + - - +
109l LEU* 4.1 6.7 - - - +
111l LEU* 1.3 76.4 - - - +
113l CYS* 1.3 50.1 + - - +
115l GLU* 3.1 19.5 - - - +
116l TRP* 2.5 37.7 + - - +
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Residues in contact with CYS 113 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89l VAL* 6.4 2.5 - - + -
93l LEU* 5.2 8.3 - - + -
109l LEU 3.8 8.8 + - - +
110l CYS* 3.2 17.3 + - - +
111l LEU 3.1 0.8 - - - -
112l GLU* 1.3 77.4 - - - +
114l ILE* 1.3 60.4 + - - +
116l TRP* 3.7 10.0 - - + +
117l ALA* 2.9 29.0 + - - +
125l LEU* 5.6 0.9 - - - +
129l LEU* 4.5 20.2 - - + +
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Residues in contact with ILE 114 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110l CYS 2.9 18.5 + - - +
111l LEU* 3.1 7.8 + - - +
113l CYS* 1.3 75.7 - - - +
115l GLU* 1.3 59.2 + - - +
117l ALA* 3.1 5.8 + - - +
118l LYS* 3.0 47.4 + - - +
126l ARG* 3.7 15.3 - - + +
129l LEU* 3.7 29.4 - - + -
130l GLU* 3.7 37.7 - - + +
133l LEU* 3.7 18.4 - - + -
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Residues in contact with GLU 115 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111l LEU 3.0 21.0 + - - +
112l GLU* 3.1 23.7 - - - +
114l ILE* 1.3 77.1 - - - +
116l TRP* 1.3 69.2 + - - +
118l LYS* 3.4 29.4 + - + +
119l SER* 3.3 17.2 + - - -
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Residues in contact with TRP 116 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74l ARG* 3.1 46.4 - - + -
75l PRO* 5.3 0.2 - - + -
76l PHE* 4.8 4.5 - - + -
77l LEU* 4.3 22.2 - - + -
85l ALA* 6.4 0.2 - - - +
89l VAL* 5.5 13.4 - - + +
112l GLU 2.5 27.6 + - - +
113l CYS* 3.7 8.3 - - + -
114l ILE 3.1 0.2 - - - -
115l GLU* 1.3 85.2 - - - +
117l ALA* 1.3 59.6 + - - +
118l LYS 3.1 0.4 - - - -
119l SER* 3.0 26.1 + - - -
120l GLU* 2.8 52.8 + - - +
125l LEU* 6.1 3.8 - - + -
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Residues in contact with ALA 117 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113l CYS 2.9 20.6 + - - +
114l ILE* 3.1 5.8 + - - +
116l TRP* 1.3 74.8 - - + +
118l LYS* 1.3 64.7 + - - +
120l GLU* 4.3 4.7 - - - -
121l LYS* 3.5 2.4 + - - -
122l ARG* 3.4 34.0 + - + +
125l LEU* 4.5 17.7 - - + -
126l ARG* 3.7 30.9 - - + +
129l LEU* 6.4 0.7 - - + -
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Residues in contact with LYS 118 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114l ILE* 3.0 41.6 + - - +
115l GLU* 3.4 19.9 - - + +
116l TRP 3.1 0.2 - - - -
117l ALA* 1.3 79.3 - - - +
119l SER* 1.3 61.3 + - - +
121l LYS* 3.4 20.8 + - - +
126l ARG* 4.1 29.3 - - - +
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Residues in contact with SER 119 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115l GLU* 3.3 15.5 + - - -
116l TRP* 3.0 24.7 + - - -
118l LYS* 1.3 78.3 - - - +
120l GLU* 1.3 66.6 + - - +
121l LYS* 2.8 27.1 + - - +
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Residues in contact with GLU 120 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 5.0 0.2 - - - +
183A LEU 5.3 3.5 - - - +
77l LEU 4.4 6.9 - - - +
78l ASN* 6.5 1.1 - - - -
82l LYS* 3.7 41.0 + - + +
85l ALA* 6.5 1.1 - - - -
116l TRP* 2.8 66.5 + - - +
117l ALA* 4.1 3.3 + - - +
119l SER* 1.3 79.0 - - - +
121l LYS* 1.3 71.7 + - - +
122l ARG* 3.1 19.3 + - + +
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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