Contacts of the helix formed by residues 111 - 127 (chain A) in PDB entry 6B9H
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A LEU* 3.3 36.8 + - + +
106A ILE* 3.9 5.8 - - - +
109A HIS* 3.1 9.2 - - + +
110A SER* 1.3 72.5 - - - +
112A ALA* 1.3 59.3 + - - +
113A ALA* 2.9 23.1 + - - +
114A GLU* 3.1 26.5 + - + +
115A LEU* 3.0 25.7 + - - +
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A CYS* 3.2 28.7 - - + +
32A VAL* 4.1 19.3 - - + -
110A SER 3.1 6.3 + - - +
111A ASP* 1.3 70.9 + - - +
113A ALA* 1.3 60.1 + - - +
115A LEU* 4.0 7.4 - - - -
116A GLY 2.8 21.7 + - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 5.9 10.8 - - + +
12A LEU* 5.5 1.0 - - - +
13A CYS* 5.4 0.9 - - - -
111A ASP* 2.9 10.3 + - - +
112A ALA* 1.3 75.5 - - - +
114A GLU* 1.3 69.5 + - + +
116A GLY* 3.2 3.4 + - - -
117A ARG* 3.1 25.0 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU 4.4 1.4 - - - +
101A PRO* 3.5 13.0 - - - +
102A ASP* 2.8 45.7 + - + +
105A LEU* 4.2 8.8 - - + +
106A ILE* 3.6 22.1 - - + +
111A ASP* 3.1 26.8 + - + +
113A ALA* 1.3 75.6 - - - +
115A LEU* 1.3 66.1 + - - +
117A ARG* 3.1 18.6 + - - +
118A MET 3.0 17.3 + - - -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A CYS* 3.8 14.8 - - - -
32A VAL* 3.7 29.8 - - + +
35A LEU* 3.7 45.8 - - + +
36A THR* 5.2 2.7 - - + -
41A MET* 4.1 25.8 - - + -
106A ILE* 3.8 21.9 - - + +
110A SER 6.1 0.2 - - - -
111A ASP 3.0 17.6 + - - +
112A ALA* 3.6 5.8 - - - +
114A GLU* 1.3 77.8 - - - +
116A GLY* 1.3 63.3 + - - +
118A MET* 3.1 3.6 + - + +
119A LEU* 3.0 23.3 + - + +
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.7 15.4 - - - +
13A CYS* 3.9 26.2 - - - -
112A ALA 2.8 16.5 + - - -
113A ALA* 3.2 4.9 + - - -
115A LEU* 1.3 75.3 - - - +
117A ARG* 1.3 55.4 + - - +
119A LEU* 3.3 6.4 + - - +
120A GLN* 2.8 28.9 + - - +
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.3 4.9 - - + +
99A THR* 3.8 41.9 + - - +
101A PRO* 3.9 17.4 - - + +
113A ALA 3.1 13.5 + - - +
114A GLU* 3.1 27.7 + - - +
116A GLY* 1.3 74.2 - - - +
118A MET* 1.3 63.8 + - - +
120A GLN* 3.3 23.2 + - - +
121A LEU* 3.1 25.8 + - - +
156A GLU* 4.4 18.3 + - - -
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Residues in contact with MET 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A MET* 3.9 28.0 - - + -
76A LEU* 4.0 10.8 - - + +
79A ILE* 3.5 34.1 - - + -
80A LEU* 4.0 19.1 - - + +
83A ILE* 4.1 13.2 - - + +
101A PRO* 3.2 30.1 - - + -
103A VAL* 3.9 18.6 - - - -
106A ILE* 4.0 8.5 - - + -
114A GLU 3.0 8.0 + - - +
115A LEU* 3.1 8.3 + - - +
117A ARG* 1.3 73.9 - - - +
119A LEU* 1.3 67.2 + - - +
121A LEU* 3.1 16.5 + - + +
122A ILE* 3.1 17.8 + - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A CYS* 3.8 26.2 - - - +
16A LEU* 3.8 24.7 - - + +
17A LEU 4.0 5.6 - - - +
19A TRP* 4.5 2.8 - - + -
20A ILE* 3.9 25.4 - - + -
35A LEU* 3.9 28.0 - - + -
41A MET* 3.7 26.7 - - + -
115A LEU* 3.0 23.8 + - + +
116A GLY 3.7 5.8 - - - +
118A MET* 1.3 75.5 - - - +
120A GLN* 1.3 57.7 + - - +
122A ILE* 3.1 7.5 + - + +
123A LEU* 2.8 28.4 + - - +
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.8 16.7 - - + +
16A LEU* 3.6 12.3 - - + +
116A GLY 2.8 14.0 + - - +
117A ARG* 3.4 23.8 + - - +
119A LEU* 1.3 76.4 - - - +
121A LEU* 1.3 60.1 + - + +
123A LEU* 3.3 5.9 + - - +
124A GLY 2.9 23.2 + - - -
153A ALA* 3.1 39.8 + - + +
156A GLU* 3.0 35.7 + - - +
157A LEU* 3.5 18.1 - - + +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.7 30.1 - - + -
83A ILE* 3.9 22.2 - - + -
84A LEU* 4.9 6.1 - - + -
95A ILE* 3.7 29.6 - - + +
96A ASN 4.0 11.9 - - - +
97A ASP* 5.2 7.0 - - + -
99A THR 5.6 3.8 - - - +
100A LEU* 5.3 1.8 - - + -
101A PRO* 3.8 21.1 - - + -
117A ARG 3.1 14.6 + - - +
118A MET* 3.1 9.5 + - - +
120A GLN* 1.3 79.6 - - + +
122A ILE* 1.3 57.9 + - - +
124A GLY* 3.1 3.3 + - - +
125A CYS* 3.0 31.7 + - - -
157A LEU* 6.0 0.9 - - + -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP* 4.1 9.0 - - + -
20A ILE* 4.5 3.6 - - + -
41A MET* 3.4 53.2 - - + +
44A VAL* 3.8 16.4 - - + -
45A LEU* 4.2 11.9 - - + -
48A ILE* 3.8 24.0 - - + +
83A ILE* 3.8 20.9 - - + -
118A MET 3.1 11.9 + - - +
119A LEU* 3.1 12.8 + - + +
121A LEU* 1.3 73.2 - - - +
123A LEU* 1.3 65.2 + - - +
125A CYS* 3.0 19.9 + - - +
126A ALA 3.0 10.0 + - - -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 12.3 - - + -
19A TRP* 3.6 41.5 - - + -
119A LEU 2.8 12.7 + - - +
120A GLN* 3.4 7.9 - - - +
122A ILE* 1.3 75.5 - - - +
124A GLY* 1.3 62.1 + - - +
126A ALA* 3.1 2.9 + - - +
127A VAL* 2.9 29.8 + - + +
139A ILE* 4.0 20.9 - - + -
150A VAL* 4.0 13.0 - - + -
153A ALA* 3.8 24.7 - - + -
154A ILE* 3.8 25.4 - - + -
157A LEU* 4.3 4.7 - - + -
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Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.5 11.7 - - - +
120A GLN 2.9 12.0 + - - -
121A LEU* 3.1 5.5 + - - -
123A LEU* 1.3 75.5 - - - +
125A CYS* 1.3 61.8 + - - +
127A VAL* 4.1 2.0 - - - -
128A ASN* 2.9 30.8 + - - +
157A LEU* 3.6 30.2 - - - +
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Residues in contact with CYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.1 20.2 - - + -
48A ILE* 4.1 10.8 - - + -
83A ILE* 4.0 19.5 - - - -
86A TYR* 3.7 31.7 - - + -
91A LEU* 4.3 5.4 - - - -
95A ILE* 4.0 12.1 - - - -
121A LEU 3.0 17.0 + - - -
122A ILE* 3.0 9.2 + - - +
124A GLY* 1.3 77.7 - - - +
126A ALA* 1.3 63.0 + - - +
128A ASN 3.3 1.2 + - - -
129A CYS* 3.0 27.7 + - - +
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP* 3.6 34.3 - - + -
48A ILE* 3.9 20.8 - - + +
122A ILE 3.0 5.7 + - - -
123A LEU 3.1 4.2 + - - +
125A CYS* 1.3 77.7 - - - +
127A VAL* 1.3 61.6 + - + +
128A ASN 3.2 1.3 + - - -
129A CYS* 3.4 16.6 - - - -
132A LYS* 3.4 10.9 - - - -
135A TYR* 3.5 22.3 - - + +
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 2.9 30.7 + - + +
124A GLY* 3.9 11.2 - - - +
125A CYS 3.3 0.2 - - - -
126A ALA* 1.3 79.9 - - + +
128A ASN* 1.3 68.5 + - - +
132A LYS* 3.3 22.9 - - - +
135A TYR* 5.1 2.2 - - + -
136A ILE* 4.1 27.5 - - + +
139A ILE* 4.3 8.7 - - + -
154A ILE* 4.0 40.4 - - + -
157A LEU* 4.8 2.5 - - + -
158A MET* 5.0 3.8 - - - +
451B LEU* 5.3 3.8 - - + +
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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