Contacts of the helix formed by residues 107 - 124 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106L THR* 1.3 74.5 - - - +
108L LYS* 1.3 57.5 + - - +
109L ARG 3.1 0.4 - - - -
110L ALA* 2.9 28.3 + - + +
111L ASP* 4.5 0.4 - - - -
163L ARG* 3.6 22.5 + - - +
164L LEU 5.3 1.5 + - - -
165L LEU* 4.9 5.3 - - - +
166L VAL* 3.3 37.4 + - + +
214L ARG* 3.7 35.5 + - + +
215L ASP* 3.3 23.7 + - - +
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Residues in contact with LYS 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ALA 5.6 2.7 - - - +
27L ASP* 4.7 9.9 - - - +
30L SER* 5.6 6.3 - - - +
32L PHE* 4.3 9.7 - - + -
104L LEU* 4.2 11.7 - - + +
106L THR* 3.1 14.7 + - - +
107L GLN* 1.3 73.8 - - - +
109L ARG* 1.3 52.4 + - - +
111L ASP* 3.0 19.0 + - + +
112L TYR* 2.7 34.8 + - - +
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Residues in contact with ARG 109 (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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104L LEU* 4.0 30.4 - - + +
106L THR 3.2 15.8 + - - +
107L GLN 3.1 0.8 - - - -
108L LYS* 1.3 76.9 - - - +
110L ALA* 1.3 55.8 + - - +
112L TYR* 3.0 13.6 + - + +
113L LEU* 2.8 36.1 + - + +
164L LEU* 5.9 3.4 - - + -
166L VAL* 5.2 9.9 - - + -
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Residues in contact with ALA 110 (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 GLN* 2.9 15.1 + - + +
109L ARG* 1.3 75.5 - - - +
111L ASP* 1.3 65.5 + - - +
113L LEU* 3.0 22.1 + - - +
114L LEU* 3.0 17.4 + - - +
163L ARG* 4.1 22.4 - - + +
164L LEU* 3.4 36.7 - - + +
166L VAL* 5.6 3.1 - - + +
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Residues in contact with ASP 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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32L PHE* 4.7 9.9 - - + +
107L GLN 4.5 0.2 - - - -
108L LYS* 3.0 23.0 + - + +
110L ALA* 1.3 75.6 - - - +
112L TYR* 1.3 52.2 + - - +
114L LEU* 3.0 6.2 + - - +
115L PHE* 2.8 35.1 + - - +
143L LEU* 3.5 18.0 - - + +
144L ASN* 3.2 34.4 + - - +
163L ARG* 2.3 43.2 + - - +
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Residues in contact with TYR 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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32L PHE* 3.3 33.4 - + + -
95L VAL* 5.0 0.7 - - + -
96L ILE* 3.1 52.3 + - + +
99L PHE* 3.6 30.7 - + + +
100L ASP* 3.1 17.6 + - - -
104L LEU* 3.9 11.7 - - + -
108L LYS 2.7 12.4 + - - +
109L ARG* 3.0 18.4 + - + +
111L ASP* 1.3 76.4 - - - +
113L LEU* 1.3 66.5 + - + +
115L PHE* 3.0 10.9 + + - +
116L LYS* 2.6 40.9 + - + +
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Residues in contact with LEU 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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109L ARG* 2.8 19.3 + - + +
110L ALA* 3.0 8.0 + - - +
112L TYR* 1.3 93.7 - - + +
114L LEU* 1.3 64.2 + - + +
116L LYS* 3.0 7.8 + - + +
117L LYS* 3.0 22.3 + - - +
164L LEU* 3.6 35.9 - - + -
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Residues in contact with LEU 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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34L LEU* 5.5 1.3 - - + -
110L ALA 3.0 14.3 + - - +
111L ASP* 3.4 5.4 - - - +
113L LEU* 1.3 76.5 - - + +
115L PHE* 1.3 63.9 + - - +
117L LYS* 3.0 7.2 + - - +
118L ALA* 3.0 21.1 + - - +
139L LEU* 3.8 40.7 - - + +
142L SER* 3.4 41.1 - - - +
143L LEU* 3.8 11.7 - - + +
161L ALA* 4.2 7.9 - - + -
162L GLU 4.1 19.3 - - - +
163L ARG* 3.7 20.4 - - + +
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Residues in contact with PHE 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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32L PHE* 3.7 35.0 - + + -
33L MET 3.8 11.9 - - - -
34L LEU* 4.5 9.2 - - + -
50L PRO* 3.4 28.5 - - + -
51L ARG 3.3 24.5 - - - -
52L PHE* 5.0 0.2 - - + -
92L LEU* 3.6 32.1 - - + -
95L VAL* 5.7 1.8 - - + -
96L ILE* 4.3 20.4 - - + -
111L ASP 2.8 12.2 + - - +
112L TYR* 3.2 15.7 - + - +
114L LEU* 1.3 76.0 - - - +
116L LYS* 1.3 62.4 + - - +
118L ALA* 3.0 8.2 + - - +
119L PHE* 2.8 29.6 + - + +
143L LEU* 4.8 4.4 - - + +
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Residues in contact with LYS 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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96L ILE* 4.8 11.2 - - + -
112L TYR* 2.6 35.1 + - + +
113L LEU* 3.0 12.3 + - + +
115L PHE* 1.3 76.0 - - - +
117L LYS* 1.3 64.3 + - - +
119L PHE* 3.0 7.9 + - - +
120L TYR* 2.9 36.9 + - + -
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Residues in contact with LYS 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 LEU 3.0 11.5 + - - +
114L LEU* 3.0 8.3 + - - +
116L LYS* 1.3 74.0 - - - +
118L ALA* 1.3 64.2 + - - +
120L TYR* 3.0 9.6 + - - +
121L LEU* 3.0 27.1 + - + +
139L LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 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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34L LEU* 3.6 39.3 - - + -
114L LEU 3.0 7.4 + - - +
115L PHE 3.5 7.0 - - - +
117L LYS* 1.3 75.0 - - - +
119L PHE* 1.3 53.6 + - - +
121L LEU* 3.0 8.7 + - - +
122L ILE* 2.7 42.9 + - + +
136L ILE* 4.7 7.4 - - + -
139L LEU* 3.5 17.7 - - + +
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Residues in contact with PHE 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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50L PRO* 4.5 5.1 - - + +
89L LEU* 3.6 51.1 - - + -
92L LEU* 3.8 25.6 - - + -
93L GLU* 4.1 14.8 - - + -
96L ILE* 3.5 23.6 - - + -
115L PHE* 2.8 20.1 + + + +
116L LYS* 3.3 9.6 - - - +
118L ALA* 1.3 75.8 - - - +
120L TYR* 1.3 73.4 + + - +
122L ILE* 3.0 11.4 + - - +
123L LYS* 2.5 52.8 + - + +
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Residues in contact with TYR 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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96L ILE* 4.9 17.7 - - + +
100L ASP* 5.5 1.0 + - - -
116L LYS* 2.9 29.6 + - + +
117L LYS* 3.0 9.2 + - - +
119L PHE* 1.3 93.5 - + - +
121L LEU* 1.3 64.5 + - - +
123L LYS* 3.0 34.0 + - + +
124L ASN* 2.8 37.0 + - - +
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Residues in contact with LEU 121 (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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117L LYS* 3.0 13.2 + - + +
118L ALA* 3.3 7.0 - - - +
120L TYR* 1.3 76.0 - - + +
122L ILE* 1.3 61.2 + - - +
124L ASN* 3.5 2.4 + - - +
125L LYS 3.2 2.8 + - - -
126L GLU* 3.0 61.1 + - + +
127L HIS 3.6 3.4 + - - +
132L GLY* 4.5 4.3 - - - +
135L GLN* 4.0 34.3 - - + +
136L ILE* 3.9 28.7 - - + -
139L LEU* 3.9 23.3 - - + -
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Residues in contact with ILE 122 (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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34L LEU* 4.3 6.5 - - + -
48L VAL* 3.9 23.6 - - + +
50L PRO* 3.7 40.4 - - + -
89L LEU* 4.3 20.3 - - + +
118L ALA 2.7 28.4 + - - +
119L PHE* 3.4 6.3 - - - +
121L LEU* 1.3 71.7 - - - +
123L LYS* 1.3 66.1 + - - +
125L LYS* 2.9 16.3 + - - +
127L HIS* 3.7 25.8 + - + +
136L ILE* 3.9 17.0 - - + -
4O A 4.8 3.0 + - - +
5O T 6.0 0.2 - - - +
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Residues in contact with LYS 123 (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 LEU* 4.7 17.0 - - + +
119L PHE* 2.5 42.6 + - + +
120L TYR* 3.0 39.9 + - + +
122L ILE* 1.3 72.9 - - - +
124L ASN* 1.3 85.1 + - - +
125L LYS* 3.5 6.4 + - - +
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Residues in contact with ASN 124 (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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120L TYR* 2.8 26.3 + - - +
121L LEU* 4.1 0.6 - - - +
122L ILE 3.1 0.2 - - - -
123L LYS* 1.3 109.5 + - - +
125L LYS* 1.3 67.3 + - - +
126L GLU* 3.1 33.6 + - + +
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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