Contacts of the helix formed by residues 111 - 121 (chain A) in PDB entry 3L6B
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 PRO 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A SER* 4.2 2.0 - - - +
109A THR 3.7 2.4 - - - +
110A ALA* 1.4 90.2 - - + +
112A ASP* 1.3 66.2 + - - +
113A CYS* 4.3 11.4 - - - -
114A LYS* 3.1 26.9 + - + +
115A LYS* 3.1 11.1 + - - +
238A ASP* 3.5 43.1 - - + +
316A ASN 5.6 0.9 - - - +
318A ASP* 3.4 20.2 - - + +
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Residues in contact with ASP 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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110A ALA 3.5 2.6 + - - +
111A PRO* 1.3 71.7 - - - +
113A CYS* 1.3 63.4 + - - +
115A LYS* 3.2 22.0 + - - +
116A LEU* 2.9 39.7 + - + +
318A ASP* 2.8 14.5 + - - +
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Residues in contact with CYS 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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111A PRO* 4.3 4.3 - - - -
112A ASP* 1.3 75.3 - - - +
114A LYS* 1.3 72.1 + - - +
116A LEU* 3.6 8.3 + - - +
117A ALA* 3.0 30.0 + - - +
316A ASN* 4.0 12.3 - - - -
317A VAL 3.6 9.6 - - - +
318A ASP* 3.1 49.2 + - - +
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Residues in contact with LYS 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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84A SER* 3.5 28.5 + - - +
85A GLY* 3.9 14.9 - - - +
86A ASN* 3.4 26.4 - - - +
89A GLN* 5.5 3.3 - - - +
106A VAL* 6.1 0.4 - - + -
110A ALA* 5.2 0.7 - - + -
111A PRO* 3.1 15.9 + - + +
113A CYS* 1.3 86.1 - - - +
115A LYS* 1.3 65.3 + - - +
117A ALA* 3.4 5.7 + - - +
118A ILE* 3.1 29.9 + - - +
238A ASP* 2.7 27.3 + - - +
239A GLY* 4.5 8.3 - - - -
283A GLU* 2.7 21.7 + - - -
316A ASN* 3.3 27.1 - - + +
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Residues in contact with LYS 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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106A VAL* 4.5 2.4 - - + +
107A PRO 4.0 5.2 - - - -
108A GLN* 2.6 35.7 + - - +
110A ALA* 3.3 25.0 + - + +
111A PRO 3.1 10.1 + - - +
112A ASP* 3.6 23.6 + - - +
114A LYS* 1.3 76.4 - - - +
116A LEU* 1.3 64.4 + - + +
118A ILE* 3.4 2.0 + - - -
119A GLN* 3.0 29.0 + - - +
125A ILE* 3.7 12.7 - - + +
127A TYR* 3.5 44.8 - - + +
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Residues in contact with LEU 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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112A ASP* 2.9 31.3 + - + +
113A CYS* 3.9 6.7 - - - +
115A LYS* 1.3 75.5 - - + +
117A ALA* 1.3 59.2 + - - +
119A GLN* 3.2 19.5 + - + +
120A ALA* 2.8 29.1 + - - +
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Residues in contact with ALA 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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89A GLN* 3.7 31.0 - - - +
113A CYS 3.0 19.3 + - - +
114A LYS* 3.9 4.9 - - - +
115A LYS 3.4 0.4 - - - -
116A LEU* 1.3 72.9 - - - +
118A ILE* 1.3 66.4 + - - +
120A ALA* 3.2 8.7 + - - +
121A TYR* 3.1 32.5 + - + -
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Residues in contact with ILE 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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85A GLY* 3.9 22.4 - - - +
88A GLY* 4.0 1.1 - - - -
89A GLN* 3.8 22.7 - - + +
92A THR* 4.4 0.8 - - - +
104A ILE* 3.8 21.3 - - + -
106A VAL* 3.7 27.8 - - + -
114A LYS 3.1 18.2 + - - +
115A LYS* 3.7 7.2 - - - +
116A LEU 3.3 0.2 - - - -
117A ALA* 1.3 77.7 - - - +
119A GLN* 1.3 63.0 + - - +
121A TYR* 3.4 11.3 + - - +
122A GLY 3.5 0.2 + - - -
123A ALA* 3.3 38.0 + - + +
125A ILE* 4.0 19.5 - - + -
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Residues in contact with GLN 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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115A LYS* 3.0 26.6 + - - +
116A LEU* 3.2 20.8 + - + +
118A ILE* 1.3 78.1 - - - +
120A ALA* 1.3 58.1 + - - +
122A GLY* 2.9 21.0 + - - -
123A ALA 4.3 12.6 - - - +
125A ILE* 3.8 29.4 - - + +
127A TYR* 3.7 15.1 + - - -
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Residues in contact with ALA 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 LYS* 5.1 4.0 + - - -
116A LEU 2.8 20.1 + - - +
117A ALA* 3.2 10.7 + - - +
119A GLN* 1.3 73.1 - - - +
121A TYR* 1.3 61.1 + - + +
122A GLY* 3.3 1.4 + - - -
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Residues in contact with TYR 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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52A THR* 3.6 21.0 + - + +
89A GLN* 2.8 52.7 + - + -
92A THR* 3.4 28.5 - - + +
93A TYR* 3.7 35.1 - + + +
96A LYS* 3.6 34.6 - - + +
117A ALA* 3.1 27.7 + - + +
118A ILE 3.8 2.5 - - - +
119A GLN 3.2 0.6 - - - -
120A ALA* 1.3 76.4 - - + +
122A GLY* 1.3 56.8 + - - +
123A ALA 3.5 1.1 - - - -
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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