Contacts of the helix formed by residues 116 - 134 (chain B) in PDB entry 3LB2
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 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASN 5.9 0.9 - - - +
29A PRO* 3.6 37.8 - - + +
30A ASP* 5.4 0.7 - - - +
1B GLY* 3.9 18.6 - - - +
2B PHE 3.7 9.7 + - - +
5B ASP* 2.8 17.3 + - - +
114B SER 3.6 2.0 + - - +
115B PHE* 1.3 67.4 - - - +
117B SER* 1.3 64.2 + - - +
118B GLN* 3.8 7.6 + - - +
119B SER* 2.7 44.0 + - - -
120B TRP* 3.2 15.8 + - - -
195B SO4 3.9 4.9 + - - -
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 4.0 13.0 - - - +
108B MET* 4.0 27.8 - - - -
109B ARG* 3.4 37.2 + - - +
115B PHE 3.0 9.1 + - - -
116B ASP* 1.3 74.4 - - - +
118B GLN* 1.3 63.5 + - - +
120B TRP* 3.2 3.6 + - - +
121B ASP* 2.9 27.5 + - - +
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO* 4.5 14.3 - - - +
30A ASP* 3.9 26.0 + - - +
109B ARG* 5.7 7.4 - - - +
116B ASP* 3.2 5.2 + - - +
117B SER* 1.3 82.1 + - - +
119B SER* 1.3 58.2 + - - +
121B ASP* 3.3 8.7 + - - +
122B ARG* 3.0 37.6 + - + +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.9 24.2 - - - +
73B CYS* 3.8 8.6 - - - -
116B ASP* 2.7 34.8 + - - -
118B GLN* 1.3 76.6 - - - +
120B TRP* 1.3 59.7 + - - +
122B ARG* 3.0 31.3 + - - +
123B PHE* 2.8 28.6 + - - +
195B SO4 4.4 2.6 + - - -
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.5 32.1 - + - -
5B ASP* 2.9 38.9 + - + +
6B ILE* 4.0 9.0 - - + -
9B ILE* 4.1 9.0 - - + -
63B MET* 4.7 3.6 - - - -
64B MET* 3.7 35.4 - - + -
67B ALA* 4.0 9.9 - - + -
101B PHE* 4.1 14.6 - + + -
104B LEU* 4.8 8.5 - - + -
105B VAL* 4.0 9.9 - - + -
108B MET* 3.4 36.4 - - + +
116B ASP 3.2 24.4 + - - -
117B SER 3.2 8.1 + - - +
119B SER* 1.3 72.1 - - - +
121B ASP* 1.3 60.8 + - - +
123B PHE* 3.6 26.2 - + - +
124B GLY* 2.9 26.3 + - - -
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 5.8 1.5 - - - +
105B VAL* 3.6 19.6 - - + +
109B ARG* 3.9 18.4 + - - +
117B SER 2.9 12.7 + - - +
118B GLN* 3.4 13.2 - - - +
120B TRP* 1.3 76.3 - - - +
122B ARG* 1.3 57.0 + - + +
124B GLY* 3.3 3.2 + - - -
125B LYS* 3.0 54.8 + - - +
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 4.4 8.7 + - - +
73B CYS* 3.4 32.4 - - + +
118B GLN* 3.0 23.7 + - + +
119B SER* 3.0 36.3 + - - +
121B ASP* 1.3 75.6 - - + +
123B PHE* 1.3 57.4 + - - +
125B LYS* 3.2 11.1 + - + +
126B ASN* 2.8 41.3 + - - +
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.7 21.3 - + + -
63B MET* 4.5 9.4 - - + -
66B VAL* 3.9 12.6 - - + -
67B ALA* 3.7 32.8 - - + -
70B ALA* 4.4 2.9 - - + -
73B CYS* 3.6 27.2 - - + +
75B PRO* 4.2 22.0 - - + -
101B PHE* 3.8 32.3 - + - -
119B SER 2.8 20.5 + - - +
120B TRP* 3.6 24.9 - + - +
122B ARG* 1.3 73.2 - - - +
124B GLY* 1.3 56.7 + - - +
126B ASN* 3.2 1.6 + - - +
127B LEU* 2.8 37.4 + - + +
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.7 38.0 - - - -
120B TRP 2.9 12.3 + - - -
121B ASP 3.7 2.9 - - - -
122B ARG 3.3 0.2 - - - -
123B PHE* 1.3 77.0 - - - +
125B LYS* 1.3 56.3 + - - +
127B LEU* 3.3 3.8 + - - +
128B VAL* 2.9 35.5 + - - +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 5.2 8.0 + - + -
121B ASP* 3.0 41.8 + - - +
122B ARG* 3.2 11.9 + - + +
124B GLY* 1.3 74.4 - - - +
126B ASN* 1.3 60.6 + - - +
128B VAL* 3.4 7.7 + - - +
129B SER* 3.0 27.6 + - - -
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP 4.3 3.2 + - - -
73B CYS* 3.0 35.8 + - - +
74B VAL* 3.7 17.1 - - + +
75B PRO* 3.8 12.1 - - + +
122B ARG* 2.8 25.2 + - - +
123B PHE 3.7 0.4 - - - +
125B LYS* 1.3 76.3 - - - +
127B LEU* 1.3 61.8 + - - +
129B SER* 3.4 8.7 + - - -
130B ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 4.6 5.8 - - + -
75B PRO* 3.9 26.8 - - + +
80B ALA* 4.8 9.0 - - + -
83B LEU* 4.1 21.3 - - + -
97B PHE* 4.7 6.3 - - + -
101B PHE* 3.8 18.4 - - + -
123B PHE* 2.8 31.9 + - + +
124B GLY* 3.7 5.4 - - - +
126B ASN* 1.3 69.9 - - - +
128B VAL* 1.3 59.7 + - + +
130B ALA* 3.1 2.8 + - - +
131B LEU* 2.8 46.0 + - + +
139B HEM 3.6 31.2 - - + -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 3.8 27.7 - - + +
97B PHE* 4.1 11.9 - - + -
98B GLU* 4.1 36.8 - - + +
101B PHE* 5.6 2.0 - - + -
124B GLY 2.9 21.2 + - - +
125B LYS* 3.7 7.6 - - - +
127B LEU* 1.3 77.0 - - + +
129B SER* 1.3 61.3 + - - +
131B LEU* 3.2 9.2 + - - +
132B SER* 2.9 23.6 + - - -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS 3.0 13.8 + - - -
126B ASN* 3.5 13.5 - - - -
128B VAL* 1.3 76.6 - - - +
130B ALA* 1.3 57.8 + - - +
132B SER* 3.3 8.4 + - - -
133B SER* 2.9 34.5 + - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PRO* 4.1 19.1 - - + +
76B LEU 5.3 0.2 - - - +
77B ALA* 5.6 3.4 - - - -
80B ALA* 3.6 21.1 - - + +
126B ASN 2.9 18.1 + - - +
127B LEU 3.5 4.3 - - - +
129B SER* 1.3 75.6 - - - +
131B LEU* 1.3 59.6 + - - +
133B SER* 3.3 8.3 + - - -
134B ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ALA* 3.7 26.9 - - - +
83B LEU* 3.8 22.2 - - + -
84B VAL* 3.7 11.8 - - + +
94B THR* 4.0 10.1 - - + -
97B PHE* 3.6 46.7 - - + -
127B LEU* 2.8 31.8 + - + +
128B VAL* 3.2 9.8 + - - +
130B ALA* 1.3 72.9 - - - +
132B SER* 1.3 60.4 + - - +
134B ALA* 3.2 3.7 + - - +
135B GLY 3.1 6.6 + - - -
136B MET* 2.9 36.0 + - + +
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 4.1 7.0 - - - +
128B VAL* 2.9 13.9 + - - -
129B SER* 3.5 11.0 - - - -
131B LEU* 1.3 76.9 - - - +
133B SER* 1.3 62.7 + - - +
135B GLY* 3.0 14.9 + - - -
136B MET 3.9 15.9 + - - +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B SER* 2.9 23.2 + - - -
130B ALA* 3.3 8.7 + - - -
132B SER* 1.3 76.6 - - - +
134B ALA* 1.3 60.1 + - - +
135B GLY 3.2 0.7 + - - -
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA 5.1 1.8 - - - +
80B ALA* 4.3 2.2 - - + -
81B ASN 4.2 17.9 - - - +
84B VAL* 3.8 26.5 - - + +
85B GLN* 4.9 4.9 + - - -
130B ALA 2.9 16.9 + - - +
131B LEU 3.5 5.8 - - - +
132B SER 3.1 0.4 - - - -
133B SER* 1.3 77.9 - - - +
135B GLY* 1.3 57.5 + - - +
136B MET 3.7 0.4 - - - -
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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