Contacts of the helix formed by residues 99 - 114 (chain A) in PDB entry 1QQG
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 SER 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A HIS* 3.3 25.3 + - - +
97A ALA* 3.3 2.1 - - - +
98A ASP* 1.3 89.7 + - - +
100A GLU* 1.3 59.8 + - - +
101A ALA* 3.4 9.9 + - - +
102A GLU* 3.1 19.6 + - - +
103A GLN 3.1 22.0 + - - -
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Residues in contact with GLU 100 (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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74A LYS* 5.9 3.1 - - - +
82A HIS* 3.3 22.2 + - + +
99A SER* 1.3 72.5 - - - +
101A ALA* 1.3 64.9 + - - +
103A GLN* 3.7 13.7 - - - +
104A ASP* 3.0 24.5 + - + +
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Residues in contact with ALA 101 (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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99A SER* 3.2 9.5 + - - +
100A GLU* 1.3 79.7 - - - +
102A GLU* 1.3 56.6 + - - +
104A ASP* 3.1 7.8 + - - +
105A SER* 2.8 28.2 + - - -
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Residues in contact with GLU 102 (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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18A TYR 4.2 7.4 - - - +
19A LEU* 3.5 22.7 - - - +
97A ALA* 3.5 5.3 - - + -
98A ASP* 3.2 41.7 + - - +
99A SER* 3.1 16.5 + - - +
101A ALA* 1.3 73.5 - - - +
103A GLN* 1.3 65.9 + - - +
105A SER* 3.3 7.1 + - - -
106A TRP* 3.1 46.4 + - + +
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Residues in contact with GLN 103 (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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74A LYS* 3.4 29.7 - - + +
75A ARG 3.3 16.0 + - - -
81A LYS 4.6 1.9 + - - +
82A HIS* 3.7 21.9 - - + +
83A LEU 2.7 31.3 + - - +
84A VAL* 3.3 14.6 - - + +
97A ALA* 3.5 8.0 - - - +
99A SER 3.1 16.8 + - - +
100A GLU* 3.7 23.8 - - - +
102A GLU* 1.3 75.7 - - - +
104A ASP* 1.3 58.4 + - - +
106A TRP* 4.9 0.2 - - - -
107A TYR* 2.9 30.3 + - - +
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Residues in contact with ASP 104 (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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74A LYS* 2.8 35.0 + - - +
100A GLU* 3.0 20.1 + - + +
101A ALA* 3.1 5.9 + - - +
103A GLN* 1.3 76.8 - - - +
105A SER* 1.3 60.9 + - - +
107A TYR* 3.6 0.2 - - - +
108A GLN* 2.9 60.7 + - - +
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Residues in contact with SER 105 (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 LYS* 3.0 25.8 + - - -
101A ALA 2.8 13.2 + - - -
102A GLU* 3.5 13.0 - - - -
104A ASP* 1.3 79.5 + - - +
106A TRP* 1.3 56.4 + - - +
108A GLN* 3.9 4.5 - - - +
109A ALA* 3.0 28.8 + - - +
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Residues in contact with TRP 106 (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 LYS* 3.7 44.4 - - + +
16A VAL 3.9 19.5 - - - -
17A GLY* 3.9 9.5 - - - -
19A LEU* 3.3 36.8 - - + +
30A PHE* 3.9 25.4 - - + -
32A LEU* 4.2 15.0 - - + -
44A LEU* 4.1 24.2 - - + -
84A VAL* 4.4 4.0 - - + -
95A ILE* 4.3 15.7 - - + -
97A ALA* 5.3 2.2 - - + -
102A GLU* 3.1 39.4 + - + +
103A GLN 3.9 2.9 - - - +
105A SER* 1.3 75.3 - - - +
107A TYR* 1.3 61.1 + - - +
109A ALA* 3.2 0.9 + - - +
110A LEU* 2.9 41.1 + - + +
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Residues in contact with TYR 107 (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 ILE* 3.7 36.6 + - + +
73A ASN* 4.2 7.1 + - - -
74A LYS* 3.3 41.7 - - + -
84A VAL* 4.2 13.6 - - + +
103A GLN 2.9 19.3 + - - +
104A ASP 3.6 3.1 - - - +
105A SER 3.3 0.2 - - - -
106A TRP* 1.3 77.7 - - - +
108A GLN* 1.3 87.3 + - - +
110A LEU* 3.7 3.3 + - - +
111A LEU* 3.2 55.6 + - + +
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Residues in contact with GLN 108 (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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74A LYS* 4.7 0.8 - - - +
104A ASP* 2.9 40.5 + - - +
105A SER* 3.9 4.5 - - - +
107A TYR* 1.3 104.6 - - - +
109A ALA* 1.3 59.5 + - - +
111A LEU* 3.2 13.5 + - - +
112A GLN* 2.8 49.2 + - - +
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Residues in contact with ALA 109 (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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14A ARG* 6.1 0.7 - - + -
15A LYS* 3.6 26.5 - - + -
32A LEU* 3.6 22.6 - - + +
105A SER 3.0 18.3 + - - +
106A TRP* 3.7 2.9 - - - +
108A GLN* 1.3 74.1 - - - +
110A LEU* 1.3 64.9 + - - +
112A GLN* 3.0 29.6 + - - +
113A LEU* 3.2 11.3 + - - +
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Residues in contact with LEU 110 (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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32A LEU* 4.0 20.8 - - + +
44A LEU* 4.3 21.5 - - + -
66A LEU* 4.0 29.9 - - + +
72A ILE* 4.1 18.4 - - + +
84A VAL* 3.6 28.7 - - + -
86A LEU* 4.4 17.3 - - + -
95A ILE* 4.7 9.6 - - + -
106A TRP* 2.9 26.7 + - + +
107A TYR 3.8 4.0 - - - +
109A ALA* 1.3 76.6 - - - +
111A LEU* 1.3 56.9 + - - +
113A LEU* 3.6 0.9 + - - -
114A HIS* 3.0 28.5 + - - +
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Residues in contact with LEU 111 (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 ILE* 4.4 26.2 - - + +
107A TYR* 3.2 58.8 + - + +
108A GLN* 3.5 20.4 - - - +
109A ALA 3.2 0.6 - - - -
110A LEU* 1.3 73.5 - - - +
112A GLN* 1.3 66.7 + - + +
114A HIS* 3.3 24.4 + - + +
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Residues in contact with GLN 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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108A GLN* 2.8 41.3 + - - +
109A ALA* 3.0 19.3 + - - +
111A LEU* 1.3 79.3 - - + +
113A LEU* 1.3 66.7 + - + +
114A HIS 4.5 2.1 - - - -
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Residues in contact with LEU 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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14A ARG* 3.8 26.5 - - + +
32A LEU* 3.7 21.8 - - + -
33A ARG 3.4 33.7 - - - +
34A ALA* 3.7 14.8 - - + +
35A ALA 5.5 0.2 - - - +
42A ALA* 4.6 9.5 - - + +
66A LEU* 3.4 22.3 - - + +
109A ALA 3.2 11.3 + - - +
112A GLN* 1.3 80.6 - - + +
114A HIS* 1.3 62.8 + - - +
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Residues in contact with HIS 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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66A LEU* 3.1 31.0 + - + +
67A GLU* 4.5 7.1 + - - -
69A CYS* 2.7 29.9 + - + -
70A PHE* 4.6 7.7 + - - -
71A ASN* 5.6 0.9 - - - -
72A ILE* 3.8 24.2 - - + -
110A LEU 3.0 20.5 + - - +
111A LEU* 3.3 22.4 + - + +
112A GLN 3.3 2.8 - - - -
113A LEU* 1.3 82.8 - - - +
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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