Contacts of the helix formed by residues 107 - 124 (chain A) in PDB entry 6BCH
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A THR* 1.3 69.8 - - - +
108A LYS* 1.3 59.8 + - - +
109A ARG 3.1 2.7 - - - -
110A ALA* 2.9 28.1 + - + +
111A ASP* 4.5 0.4 - - - -
163A ARG* 3.6 17.1 + - - +
164A LEU 5.3 1.8 + - - -
165A LEU* 4.9 5.1 - - - +
166A VAL* 3.3 38.0 + - - +
214A ARG* 3.5 65.0 + - + +
215A ASP* 3.2 23.3 + - - +
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.3 19.5 - - - +
27A ASP* 3.6 13.9 - - - +
28A ALA 4.8 4.5 + - - -
30A SER* 2.5 46.7 + - - +
31A SER* 4.5 1.6 - - - +
32A PHE* 3.7 26.5 - - + +
104A LEU* 4.1 9.9 - - + -
106A THR* 3.0 11.3 + - - +
107A GLN* 1.3 75.2 - - - +
109A ARG* 1.3 52.7 + - - +
111A ASP* 3.0 17.4 + - + +
112A TYR* 2.6 34.0 + - - +
214A ARG* 4.5 10.0 - - - +
17X A 5.8 0.8 - - - -
18X G 3.6 15.0 + - - -
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Residues in contact with ARG 109 (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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104A LEU* 4.1 28.8 - - + +
106A THR 3.2 14.5 + - - +
107A GLN 3.1 0.2 - - - -
108A LYS* 1.3 76.6 - - - +
110A ALA* 1.3 56.1 + - - +
112A TYR* 3.0 13.1 + - + +
113A LEU* 2.8 37.4 + - + +
164A LEU* 5.7 3.6 - - + -
166A VAL* 5.1 11.0 - - + -
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Residues in contact with ALA 110 (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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107A GLN* 2.9 14.4 + - + +
109A ARG* 1.3 75.1 - - - +
111A ASP* 1.3 65.5 + - - +
113A LEU* 3.0 14.0 + - - +
114A LEU* 3.0 25.9 + - - +
163A ARG* 4.0 22.9 - - + +
164A LEU* 3.3 36.5 - - + +
166A VAL* 5.7 3.0 - - + +
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Residues in contact with ASP 111 (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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32A PHE* 4.8 5.6 - - + -
108A LYS* 3.0 27.8 + - + +
110A ALA* 1.3 75.7 - - - +
112A TYR* 1.3 52.5 + - - +
114A LEU* 3.0 5.6 + - - +
115A PHE* 2.8 35.9 + - - +
143A LEU* 3.6 17.7 - - + +
144A ASN* 3.2 35.3 + - - +
163A ARG* 2.3 42.6 + - - +
214A ARG* 4.9 5.7 + - - -
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.4 32.3 - + + -
95A VAL* 5.0 0.7 - - + -
96A ILE* 3.0 51.6 + - + +
99A PHE* 3.5 33.8 - + + +
100A ASP* 3.1 16.6 + - - -
104A LEU* 3.9 15.0 - - + -
108A LYS 2.6 16.1 + - - +
109A ARG* 3.0 13.2 + - + +
111A ASP* 1.3 72.6 - - - +
113A LEU* 1.3 63.2 + - + +
115A PHE* 3.0 10.1 + + - +
116A LYS* 2.5 51.3 + - + +
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Residues in contact with LEU 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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109A ARG* 2.8 19.5 + - + +
110A ALA* 3.0 7.8 + - - +
112A TYR* 1.3 90.2 - - + +
114A LEU* 1.3 63.6 + - + +
116A LYS* 3.0 18.9 + - + +
117A LYS* 2.9 23.2 + - - +
164A LEU* 3.7 34.8 - - + -
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Residues in contact with LEU 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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34A LEU* 5.4 1.3 - - + -
110A ALA 3.0 14.5 + - - +
111A ASP* 3.4 5.2 - - - +
113A LEU* 1.3 76.1 - - + +
115A PHE* 1.3 63.6 + - - +
117A LYS* 3.0 6.3 + - - +
118A ALA* 3.0 21.9 + - - +
139A LEU* 3.7 43.3 - - + +
142A SER* 3.4 41.3 - - - +
143A LEU* 3.7 11.4 - - + +
161A ALA* 4.1 8.5 - - + -
162A GLU 4.1 18.2 - - - +
163A ARG* 3.7 19.5 - - + +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.6 37.7 - + + -
33A MET 3.8 12.1 - - - -
34A LEU* 4.5 9.2 - - + -
50A PRO* 3.5 19.7 - - + -
51A ARG 3.2 35.0 - - - -
92A LEU* 3.6 32.1 - - + -
95A VAL* 5.6 1.8 - - + -
96A ILE* 4.3 20.0 - - + -
111A ASP 2.8 12.2 + - - +
112A TYR* 3.2 13.5 - + - +
114A LEU* 1.3 75.4 - - - +
116A LYS* 1.3 62.1 + - - +
118A ALA* 3.1 8.0 + - - +
119A PHE* 2.8 30.2 + - + +
143A LEU* 4.7 4.6 - - + +
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Residues in contact with LYS 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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96A ILE* 4.0 16.2 - - + +
100A ASP* 3.7 24.6 + - - -
112A TYR* 2.5 41.9 + - + +
113A LEU* 3.0 18.8 + - + +
115A PHE* 1.3 78.7 - - - +
117A LYS* 1.3 64.6 + - - +
119A PHE* 3.1 6.6 + - - +
120A TYR* 3.0 62.4 + - + -
40H SER* 4.4 9.8 + - - -
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Residues in contact with LYS 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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113A LEU 2.9 12.0 + - - +
114A LEU* 3.5 7.6 - - - +
116A LYS* 1.3 74.8 - - - +
118A ALA* 1.3 65.1 + - - +
120A TYR* 3.0 10.1 + - - +
121A LEU* 3.0 25.8 + - + +
139A LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 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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34A LEU* 3.6 39.0 - - + -
114A LEU 3.0 6.9 + - - +
115A PHE 3.5 7.2 - - - +
117A LYS* 1.3 74.9 - - - +
119A PHE* 1.3 53.7 + - - +
121A LEU* 3.0 8.7 + - - +
122A ILE* 2.7 43.1 + - + +
136A ILE* 4.7 7.2 - - + -
139A LEU* 3.5 17.2 - - + +
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Residues in contact with PHE 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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50A PRO* 4.5 5.8 - - + +
89A LEU* 3.5 52.5 - - + -
92A LEU* 3.9 25.6 - - + -
93A GLU* 4.2 14.1 - - + -
96A ILE* 3.6 24.9 - - + -
115A PHE* 2.8 20.3 + + + +
116A LYS 3.4 7.9 - - - +
118A ALA* 1.3 76.2 - - - +
120A TYR* 1.3 74.9 + + - +
122A ILE* 3.0 11.6 + - - +
123A LYS* 2.5 53.1 + - + +
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Residues in contact with TYR 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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96A ILE* 4.9 8.1 - - + +
100A ASP* 5.5 0.3 + - - -
116A LYS* 3.0 51.9 + - + +
117A LYS* 3.0 11.0 + - - +
119A PHE* 1.3 96.6 - + - +
121A LEU* 1.3 62.9 + - - +
123A LYS* 3.0 35.0 + - + +
124A ASN* 2.8 37.2 + - - +
38H LYS* 5.5 6.9 - - - +
22K C 6.0 2.0 - - - -
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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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117A LYS* 3.0 12.4 + - + +
118A ALA* 3.0 7.3 + - - +
120A TYR* 1.3 75.2 - - + +
122A ILE* 1.3 60.5 + - - +
124A ASN* 3.5 2.6 + - - +
125A LYS 3.2 2.9 + - - -
126A GLU* 3.0 61.5 + - + +
127A HIS 3.6 3.2 + - - +
132A GLY* 4.5 4.3 - - - +
135A GLN* 4.0 34.3 - - + +
136A ILE* 3.9 23.8 - - + -
139A LEU* 3.9 27.8 - - + -
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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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34A LEU* 4.3 6.7 - - + -
48A VAL* 3.8 24.5 - - + +
50A PRO* 3.8 39.0 - - + -
89A LEU* 4.4 20.1 - - + +
118A ALA 2.7 28.0 + - - +
119A PHE* 3.4 6.5 - - - +
121A LEU* 1.3 71.3 - - - +
123A LYS* 1.3 65.7 + - - +
125A LYS* 2.9 16.3 + - - +
127A HIS* 3.6 26.5 + - + +
136A ILE* 3.9 17.0 - - + -
4C A 4.8 2.8 + - - +
5C T 6.0 0.2 - - - +
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Residues in contact with LYS 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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89A LEU* 4.7 16.5 - - + +
119A PHE* 2.5 41.8 + - + +
120A TYR* 3.0 40.4 + - + +
122A ILE* 1.3 73.3 - - - +
124A ASN* 1.3 84.1 + - - +
125A LYS* 3.5 6.4 + - - +
21K G 5.5 4.0 + - - -
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Residues in contact with ASN 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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120A TYR* 2.8 26.3 + - - +
121A LEU* 4.1 0.6 - - - +
122A ILE 3.1 0.2 - - - -
123A LYS* 1.3 108.7 + - - +
125A LYS* 1.3 67.4 + - - +
126A GLU* 3.1 32.2 + - + +
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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
------------------------------------------------------------
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