Contacts of the helix formed by residues 99 - 114 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B HIS* 3.5 17.0 + - - +
97B ALA* 3.3 2.1 + - - +
98B ASP* 1.3 90.6 + - - +
100B GLU* 1.3 59.3 + - - +
101B ALA* 3.5 10.0 + - - +
102B GLU* 3.0 20.6 + - - +
103B GLN* 2.9 28.9 + - - +
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Residues in contact with GLU 100 (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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82B HIS* 3.3 21.8 + - + +
99B SER* 1.3 74.0 - - - +
101B ALA* 1.3 58.8 + - - +
103B GLN* 3.5 13.7 - - - +
104B ASP* 2.9 32.5 + - + +
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Residues in contact with ALA 101 (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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99B SER* 3.2 9.1 - - - +
100B GLU* 1.3 81.3 - - - +
102B GLU* 1.3 62.2 + - - +
104B ASP* 3.4 4.8 + - - +
105B SER* 3.1 22.6 + - - -
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Residues in contact with GLU 102 (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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15B LYS* 6.2 0.2 - - - +
18B TYR 4.5 7.2 - - - +
19B LEU* 3.3 22.8 - - - +
97B ALA* 3.3 5.5 - - + -
98B ASP* 2.8 42.2 + - - +
99B SER* 3.0 21.1 + - - +
101B ALA* 1.3 73.4 - - - +
103B GLN* 1.3 66.5 + - - +
105B SER* 3.2 7.3 + - - -
106B TRP* 3.1 38.4 + - + +
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Residues in contact with GLN 103 (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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74B LYS* 3.6 30.7 - - + +
75B ARG 3.4 8.3 + - - -
81B LYS 4.4 1.8 + - - -
82B HIS* 3.4 29.7 - - + +
83B LEU 2.9 29.8 + - - +
84B VAL* 3.5 13.7 - - + +
97B ALA* 3.5 10.5 - - + +
99B SER 2.9 18.2 + - - +
100B GLU* 3.5 20.8 - - - +
102B GLU* 1.3 77.3 - - - +
104B ASP* 1.3 56.2 + - - +
106B TRP 3.6 0.2 + - - -
107B TYR* 3.0 29.5 + - - +
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Residues in contact with ASP 104 (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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74B LYS* 3.0 28.1 + - - +
100B GLU* 2.9 18.6 + - + +
101B ALA* 3.8 5.4 - - - +
102B GLU 3.2 0.2 - - - -
103B GLN* 1.3 76.2 - - - +
105B SER* 1.3 55.4 + - - +
107B TYR* 4.1 0.2 - - - -
108B GLN* 2.7 75.3 + - - +
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Residues in contact with SER 105 (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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14B ARG* 5.2 4.3 + - - -
15B LYS* 3.0 29.1 + - - +
101B ALA 3.1 14.6 + - - -
102B GLU* 3.2 12.5 + - - -
104B ASP* 1.3 76.8 + - - +
106B TRP* 1.3 56.4 + - - +
108B GLN* 3.7 4.7 - - - +
109B ALA* 2.8 30.7 + - - +
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Residues in contact with TRP 106 (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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15B LYS* 3.5 48.5 - - + +
16B VAL 3.9 5.8 + - - -
17B GLY* 3.9 23.6 - - - -
19B LEU* 3.6 37.0 - - + +
30B PHE* 3.8 21.1 - - + -
32B LEU* 4.2 18.2 - - + -
44B LEU* 3.9 27.6 - - + -
84B VAL* 4.6 5.4 - - + -
95B ILE* 4.6 14.4 - - + -
97B ALA* 5.4 0.9 - - + -
102B GLU* 3.1 37.6 + - + +
103B GLN 4.0 2.9 - - - +
105B SER* 1.3 75.0 - - - +
107B TYR* 1.3 67.1 + - - +
109B ALA* 3.2 1.6 + - - +
110B LEU* 2.9 33.8 + - + +
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Residues in contact with TYR 107 (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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72B ILE* 3.6 40.8 + - + -
73B ASN* 4.1 12.9 + - - -
74B LYS* 3.0 45.1 - - + -
84B VAL* 4.2 13.5 - - + +
103B GLN 3.0 19.8 + - - +
104B ASP 3.7 1.8 - - - +
106B TRP* 1.3 77.6 - - - +
108B GLN* 1.3 86.4 + - - +
110B LEU* 3.4 4.8 + - - +
111B LEU* 3.2 48.2 + - + +
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Residues in contact with GLN 108 (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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14B ARG* 6.1 0.9 - - - +
74B LYS* 4.0 1.4 - - - +
104B ASP* 2.7 58.4 + - - +
105B SER* 3.7 5.2 - - - +
107B TYR* 1.3 96.7 - - - +
109B ALA* 1.3 65.3 + - - +
111B LEU* 3.4 11.5 + - - +
112B GLN* 3.0 24.4 + - - +
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Residues in contact with ALA 109 (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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14B ARG* 4.1 15.6 - - - +
15B LYS* 3.6 23.6 - - + -
32B LEU* 3.7 17.0 - - + -
105B SER 2.8 21.2 + - - +
106B TRP* 3.2 4.5 + - + +
108B GLN* 1.3 71.1 - - - +
110B LEU* 1.3 64.5 + - - +
112B GLN* 3.0 28.8 + - - +
113B LEU* 3.2 13.0 + - - +
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Residues in contact with LEU 110 (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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32B LEU* 4.1 22.0 - - + -
44B LEU* 4.3 20.4 - - + -
66B LEU* 3.5 32.2 - - + +
72B ILE* 4.0 18.4 - - + -
84B VAL* 3.8 26.5 - - + -
86B LEU* 4.2 17.0 - - + -
95B ILE* 4.9 6.1 - - + -
106B TRP* 2.9 25.8 + - + +
107B TYR* 3.6 3.8 - - - +
109B ALA* 1.3 76.4 - - - +
111B LEU* 1.3 50.8 + - - +
113B LEU* 3.1 3.6 + - - -
114B HIS* 2.8 36.8 + - - +
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Residues in contact with LEU 111 (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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72B ILE* 4.3 25.4 - - + +
107B TYR* 3.2 52.0 + - + +
108B GLN* 3.9 14.4 - - - +
110B LEU* 1.3 70.6 - - - +
112B GLN* 1.3 65.0 + - - +
113B LEU 3.0 2.9 + - - -
114B HIS* 3.3 31.5 + - + -
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Residues in contact with GLN 112 (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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14B ARG* 2.9 48.5 + - - +
108B GLN 3.0 12.3 + - - +
109B ALA* 3.0 14.6 + - - +
111B LEU* 1.3 76.6 - - - +
113B LEU* 1.3 68.4 + - + +
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Residues in contact with LEU 113 (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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14B ARG* 3.9 22.4 - - + -
32B LEU* 3.5 33.7 - - + -
33B ARG 3.9 2.0 - - - +
34B ALA* 3.9 29.6 - - + -
42B ALA* 4.3 13.5 - - + +
66B LEU* 3.6 19.0 - - + +
109B ALA 3.6 9.9 - - - +
110B LEU 3.1 2.5 + - - +
111B LEU 3.0 0.2 - - - -
112B GLN* 1.3 103.8 - - + +
114B HIS* 1.3 59.9 + - - +
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Residues in contact with HIS 114 (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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66B LEU* 3.2 31.4 + - + -
67B GLU* 4.7 5.2 + - - -
69B CYS* 2.9 30.7 + - + -
70B PHE 4.6 7.1 + - - -
71B ASN* 5.3 0.6 - - - -
72B ILE* 3.8 28.0 - - + +
110B LEU 2.8 20.5 + - - +
111B LEU* 3.3 24.3 + - + -
113B LEU* 1.3 81.8 - - - +
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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