Contacts of the helix formed by residues 114 - 129 (chain A) in PDB entry 1Q8G
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 LYS 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A CYS* 3.7 10.7 - - + -
105A ALA* 3.6 38.2 + - - +
106A PRO 4.0 8.4 + - - +
107A GLU* 4.5 15.5 - - + +
109A ALA* 3.3 28.9 - - + +
110A PRO 3.1 18.4 - - - +
111A LEU* 3.9 7.2 - - + +
113A SER* 1.3 76.6 - - - +
115A MET* 1.3 68.3 + - - +
116A ILE 3.0 4.1 + - - +
117A TYR* 3.2 4.8 + - - -
118A ALA* 2.9 44.3 + - - +
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Residues in contact with MET 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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111A LEU* 3.4 52.3 + - + +
114A LYS* 1.3 79.0 - - - +
116A ILE* 1.3 66.2 + - + +
118A ALA* 4.3 4.0 - - - +
119A SER* 3.2 25.3 + - - -
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Residues in contact with ILE 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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4A GLY 3.3 25.4 - - - +
5A VAL* 3.9 20.0 - - + -
40A LEU* 4.2 17.3 - - + -
44A LYS* 2.7 47.8 - - + +
111A LEU 5.7 0.2 - - - +
112A LYS 4.3 14.8 - - - +
113A SER* 4.6 7.9 - - - -
114A LYS 3.0 1.9 - - - +
115A MET* 1.3 77.6 - - + +
117A TYR* 1.3 55.7 + - - +
119A SER* 2.8 8.0 + - - -
120A SER* 2.4 36.5 + - - -
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Residues in contact with TYR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.9 7.0 - - + +
80A CYS* 3.1 29.8 - - - +
81A ARG* 3.0 34.5 + - - -
82A TYR* 3.0 55.0 + + - -
103A PHE* 2.7 50.8 - + - -
104A TRP 3.3 3.2 + - - -
105A ALA* 3.6 19.1 - - + -
113A SER 4.7 3.6 - - - +
114A LYS* 3.2 8.5 + - - +
116A ILE* 1.3 77.8 - - - +
118A ALA* 1.3 59.2 + - - +
120A SER* 2.6 3.1 + - - -
121A LYS* 2.6 34.4 + - + -
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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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114A LYS* 2.9 36.6 + - - +
115A MET* 4.3 4.0 - - - +
117A TYR* 1.3 82.0 - - - +
119A SER* 1.3 59.2 + - - +
120A SER 3.3 1.7 + - - -
121A LYS* 3.6 16.4 + - - +
122A ASP 5.1 0.2 + - - -
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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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3A SER* 5.3 11.5 - - - -
4A GLY 5.9 0.6 + - - -
5A VAL* 5.1 2.6 - - - +
115A MET 3.2 17.3 + - - -
116A ILE* 2.8 8.4 + - - -
118A ALA* 1.3 76.2 - - - +
120A SER* 1.3 56.9 + - - +
121A LYS 3.6 0.2 - - - -
122A ASP* 4.9 5.0 + - - +
123A ALA* 5.0 3.6 + - - +
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Residues in contact with SER 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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5A VAL* 3.8 22.5 - - - +
47A ILE* 3.3 16.9 - - - +
82A TYR* 2.5 23.6 + - - -
116A ILE* 2.4 28.8 + - - -
117A TYR* 2.6 6.9 + - - -
119A SER* 1.3 75.5 - - - +
121A LYS* 1.3 51.4 + - - +
122A ASP 2.7 8.4 + - - -
123A ALA* 2.6 29.1 + - - -
124A ILE* 2.9 9.4 + - - +
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Residues in contact with LYS 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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82A TYR* 4.5 0.7 - - - -
103A PHE* 3.3 35.4 - - + -
117A TYR* 2.6 13.4 + - + +
118A ALA* 3.6 15.9 + - - +
120A SER* 1.3 73.5 - - - +
122A ASP* 1.3 66.6 + - - +
124A ILE* 2.8 23.6 - - - +
125A LYS* 3.8 9.5 + - - +
134A GLU* 5.5 7.0 - - - -
136A GLN* 4.4 21.4 - - - +
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Residues in contact with ASP 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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119A SER 4.9 4.6 + - - +
120A SER 2.7 5.0 + - - -
121A LYS* 1.3 88.1 + - - +
123A ALA* 1.3 64.4 + - - +
124A ILE 3.2 1.8 - - - -
125A LYS* 3.1 26.4 + - + +
126A LYS* 3.0 20.3 + - - +
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Residues in contact with ALA 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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3A SER* 5.7 4.7 - - - -
5A VAL* 3.1 36.8 - - + +
7A VAL* 4.3 13.9 - - + +
47A ILE* 5.4 1.3 - - + -
119A SER 5.0 2.2 + - - +
120A SER* 2.6 16.7 + - - +
122A ASP* 1.3 75.3 - - - +
124A ILE* 1.3 57.0 + - - +
126A LYS* 2.9 30.3 - - + +
127A LYS 4.1 0.9 + - - -
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Residues in contact with ILE 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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7A VAL* 4.7 3.6 - - - -
11A VAL* 4.7 3.1 - - + -
38A PHE* 5.5 0.7 - - + -
47A ILE* 4.3 13.9 - - + +
82A TYR* 3.5 24.2 - - + -
101A PHE* 3.3 28.0 - - + -
103A PHE* 3.5 19.1 - - + -
120A SER* 2.9 9.1 + - - +
121A LYS* 2.8 35.9 - - - +
123A ALA* 1.3 74.1 - - - +
125A LYS* 1.3 59.5 + - + +
126A LYS 3.0 4.3 - - - -
127A LYS* 2.7 58.9 - - - +
128A LEU* 3.3 14.0 + - + +
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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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103A PHE* 6.3 0.9 - - + -
121A LYS* 4.0 7.2 - - + +
122A ASP* 3.1 41.4 + - - +
124A ILE* 1.3 76.7 - - + +
126A LYS* 1.3 57.4 + - - +
127A LYS 2.9 5.6 - - - -
128A LEU* 3.5 18.8 - - + -
129A THR* 2.7 31.7 + - - -
130A GLY* 3.9 27.5 + - - +
131A ILE* 5.5 3.1 - - + +
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Residues in contact with LYS 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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122A ASP 3.0 12.1 + - - +
123A ALA* 2.9 24.2 - - + +
124A ILE 3.0 0.6 - - - -
125A LYS* 1.3 78.3 - - - +
127A LYS* 1.3 55.4 + - - +
129A THR* 4.4 4.6 + - - +
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Residues in contact with LYS 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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7A VAL* 3.4 30.7 - - + -
11A VAL* 3.0 36.5 + - - +
12A ILE* 3.1 47.5 - - + +
15A PHE* 5.6 1.1 - - - +
38A PHE* 6.0 0.6 - - - -
47A ILE* 4.6 0.7 - - - -
101A PHE* 5.0 0.8 - - - -
123A ALA 4.5 0.4 - - - +
124A ILE* 2.7 41.3 - - - +
126A LYS* 1.3 79.1 - - - +
128A LEU* 1.3 84.4 + - + +
129A THR* 3.0 15.4 + - - -
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Residues in contact with LEU 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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15A PHE* 3.5 39.1 - - + -
101A PHE* 3.0 42.0 - - + -
103A PHE* 5.4 2.5 - - + -
124A ILE* 3.3 23.6 - - + +
125A LYS* 3.1 12.9 + - + -
127A LYS* 1.3 97.6 - - + +
129A THR* 1.3 75.9 + - - +
131A ILE* 4.0 26.9 + - + +
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Residues in contact with THR 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 2.7 17.8 + - - -
126A LYS 4.8 3.7 + - - +
127A LYS 3.0 11.9 + - - -
128A LEU* 1.3 76.2 + - - +
130A GLY* 1.3 67.8 + - - +
131A ILE* 4.3 0.3 - - - -
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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