Contacts of the helix formed by residues 116 - 134 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY* 3.6 21.8 - - - -
2A PHE* 3.6 12.3 + - - +
5A ASP* 2.7 18.5 + - - +
114A SER 3.8 0.4 - - - -
115A PHE* 1.3 68.5 - - - +
117A SER* 1.3 65.2 + - - +
118A GLN* 4.1 7.8 + - - +
119A SER* 3.0 38.9 + - - -
120A TRP* 3.2 15.5 + - - -
197A SO4 3.8 4.9 + - - -
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Residues in contact with SER 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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105A VAL* 4.0 9.9 - - - +
108A MET* 4.4 17.3 - - - -
109A ARG* 2.9 49.0 + - - +
115A PHE 3.1 9.0 + - - -
116A ASP* 1.3 74.8 + - - +
118A GLN* 1.3 65.1 + - - +
120A TRP* 3.1 10.1 + - - +
121A ASP* 3.0 22.7 + - - +
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Residues in contact with GLN 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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109A ARG* 3.7 20.7 - - - +
116A ASP* 3.2 8.1 + - - +
117A SER* 1.3 82.7 + - - +
119A SER* 1.3 57.8 + - - +
121A ASP* 3.4 6.2 + - - +
122A ARG* 3.1 28.2 + - - +
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Residues in contact with SER 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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2A PHE* 3.9 14.4 - - - +
73A CYS* 3.7 21.6 - - - -
116A ASP* 3.0 33.3 + - - -
118A GLN* 1.3 76.0 - - - +
120A TRP* 1.3 62.5 + - - +
122A ARG* 3.3 18.8 + - - +
123A PHE* 2.8 30.0 + - - +
197A SO4 4.9 1.6 + - - -
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Residues in contact with TRP 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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2A PHE* 3.5 33.0 - + - -
5A ASP* 2.8 38.6 + - + +
6A ILE* 4.1 9.6 - - + -
9A ILE* 4.2 7.9 - - + -
63A MET* 4.5 5.2 - - - -
64A MET* 3.7 34.3 - - + -
67A ALA* 4.0 10.3 - - + -
101A PHE* 4.1 11.4 - + - -
104A LEU* 3.9 26.9 - - + -
105A VAL* 4.0 4.0 - - + -
108A MET* 3.4 28.6 - - + +
116A ASP 3.2 23.2 + - - -
117A SER 3.1 7.4 + - - +
119A SER* 1.3 73.3 - - - +
121A ASP* 1.3 61.0 + - - +
123A PHE* 3.6 26.7 - + - +
124A GLY* 2.9 25.5 + - - -
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Residues in contact with ASP 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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101A PHE* 5.9 1.6 - - - -
105A VAL* 3.6 25.2 - - + +
109A ARG* 4.7 8.4 + - - +
117A SER 3.0 12.4 + - - +
118A GLN* 3.6 12.1 - - - +
120A TRP* 1.3 76.8 - - - +
122A ARG* 1.3 56.8 + - - +
124A GLY* 3.2 3.2 + - - -
125A LYS* 3.0 49.0 + - - +
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Residues in contact with ARG 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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72A ASP* 3.1 29.7 + - - +
73A CYS* 3.9 10.7 - - - +
74A VAL* 5.7 0.2 - - - +
118A GLN 3.1 17.4 + - - +
119A SER* 3.9 21.6 + - - +
121A ASP* 1.3 76.7 + - - +
123A PHE* 1.3 58.7 + - - +
125A LYS* 3.2 11.4 + - + +
126A ASN* 2.9 49.9 + - - +
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Residues in contact with PHE 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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2A PHE* 3.8 17.0 - + + -
63A MET* 4.5 8.7 - - + -
66A VAL* 3.9 11.7 - - + -
67A ALA* 3.7 33.7 - - + -
70A ALA* 4.3 4.7 - - + -
73A CYS* 3.6 31.1 - - + +
75A PRO* 4.2 21.8 - - + -
101A PHE* 3.8 32.3 - + - -
119A SER 2.8 21.0 + - - +
120A TRP* 3.6 26.7 - + - +
122A ARG* 1.3 72.5 - - - +
124A GLY* 1.3 55.7 + - - +
126A ASN* 3.3 1.4 + - - +
127A LEU* 2.8 36.6 + - + +
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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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101A PHE* 3.7 39.2 - - - -
120A TRP 2.9 11.7 + - - -
121A ASP 3.2 4.2 + - - -
123A PHE* 1.3 76.5 - - - +
125A LYS* 1.3 55.6 + - - +
127A LEU* 3.3 2.2 + - - +
128A VAL* 2.9 36.1 + - - +
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Residues in contact with LYS 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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121A ASP* 3.0 33.0 + - - +
122A ARG* 3.5 15.3 - - + +
124A GLY* 1.3 75.0 - - - +
126A ASN* 1.3 65.8 + - - +
128A VAL* 3.3 8.2 + - - +
129A SER* 3.1 26.1 + - - -
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Residues in contact with ASN 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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73A CYS* 3.0 33.5 + - - +
74A VAL* 3.8 17.0 - - + +
75A PRO* 3.7 12.5 - - + +
122A ARG* 2.9 36.6 + - - +
123A PHE 3.7 0.2 - - - +
125A LYS* 1.3 76.1 - - - +
127A LEU* 1.3 61.5 + - - +
129A SER* 3.4 9.6 + - - -
130A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 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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66A VAL* 4.6 8.1 - - + -
75A PRO* 3.9 26.4 - - + +
80A ALA* 4.4 16.6 - - + -
83A LEU* 4.3 18.4 - - + -
97A PHE* 5.1 0.9 - - + -
101A PHE* 3.9 20.0 - - + -
123A PHE* 2.8 27.8 + - + +
124A GLY* 3.7 5.2 - - - +
126A ASN* 1.3 74.7 - - - +
128A VAL* 1.3 60.2 + - - +
130A ALA* 3.1 2.6 + - - +
131A LEU* 2.8 44.7 + - + +
139A HEM 3.8 28.5 - - + -
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Residues in contact with VAL 128 (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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94A THR* 3.8 24.0 - - + +
97A PHE* 4.3 9.9 - - + -
98A GLU* 3.6 51.4 - - + +
101A PHE* 5.5 2.0 - - + -
124A GLY 2.9 22.2 + - - +
125A LYS* 3.3 7.4 + - - +
127A LEU* 1.3 75.1 - - + +
129A SER* 1.3 63.1 + - - +
131A LEU* 3.2 8.7 + - + +
132A SER* 3.0 24.0 + - - -
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Residues in contact with SER 129 (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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125A LYS 3.1 15.5 + - - -
126A ASN* 3.5 13.2 + - - -
127A LEU 3.2 0.2 - - - -
128A VAL* 1.3 77.4 - - - +
130A ALA* 1.3 58.2 + - - +
132A SER* 3.3 6.6 + - - -
133A SER* 3.0 27.4 + - - -
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Residues in contact with ALA 130 (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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75A PRO* 4.4 12.3 - - + +
77A ALA* 5.2 8.5 - - + -
80A ALA* 3.5 20.9 - - + +
126A ASN 3.0 14.1 + - - +
127A LEU* 3.1 11.2 + - - +
129A SER* 1.3 74.6 - - - +
131A LEU* 1.3 63.9 + - - +
133A SER* 2.7 21.9 + - - +
134A ALA* 3.0 14.6 + - - +
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Residues in contact with LEU 131 (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 ALA* 3.6 28.3 - - - +
83A LEU* 3.9 21.8 - - + -
84A VAL* 3.7 12.4 - - + +
94A THR* 4.0 10.5 - - + -
97A PHE* 3.5 44.9 - - + -
127A LEU* 2.8 30.8 + - + +
128A VAL* 3.6 12.6 - - - +
130A ALA* 1.3 71.6 - - - +
132A SER* 1.3 63.1 + - - +
134A ALA 3.2 9.0 + - - -
135A GLY 3.2 0.7 + - - -
136A MET* 3.1 33.0 + - + +
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Residues in contact with SER 132 (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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94A THR* 4.0 10.0 - - - +
128A VAL* 3.0 13.9 + - - -
129A SER* 3.6 10.8 - - - -
130A ALA 3.3 0.2 - - - -
131A LEU* 1.3 76.5 - - - +
133A SER* 1.3 61.5 + - - +
135A GLY* 3.1 14.2 + - - -
136A MET 3.7 15.4 + - - +
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Residues in contact with SER 133 (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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77A ALA* 5.9 2.9 - - - +
129A SER 3.0 10.8 + - - -
130A ALA* 2.7 29.1 + - - -
132A SER* 1.3 77.0 - - - +
134A ALA* 1.3 56.5 + - - +
135A GLY* 3.2 3.9 + - - -
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Residues in contact with ALA 134 (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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77A ALA 5.0 1.8 - - - +
80A ALA* 4.4 1.1 - - + -
81A ASN* 3.6 43.5 + - + +
84A VAL* 3.8 17.7 - - + +
85A GLN* 4.3 3.8 + - - -
130A ALA 3.0 17.3 + - - +
131A LEU 3.2 6.2 + - - +
133A SER* 1.3 76.4 + - - +
135A GLY* 1.3 57.2 + - - +
136A MET 3.7 0.7 - - - -
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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