Contacts of the helix formed by residues 101 - 117 (chain B) in PDB entry 3QWR
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 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.7 26.0 - - + +
25B ALA 5.9 0.2 - - - -
27B SER* 3.6 25.6 - - - +
28B ALA* 3.8 20.6 - - + +
99B ASP 3.8 5.8 - - - +
100B SER* 1.4 85.2 - - - +
102B VAL* 1.3 61.5 + - + +
103B GLY 3.2 2.5 - - - -
104B GLN* 3.3 15.1 + - - +
105B LEU* 2.8 37.1 + - + +
147B LEU* 6.0 4.0 - - + -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.1 17.9 - - + +
90B PHE* 3.4 45.3 - - + -
96B LEU* 3.8 18.8 - - + -
100B SER* 3.2 20.5 + - - +
101B PRO* 1.3 78.3 - - + +
103B GLY* 1.3 57.3 + - - +
105B LEU* 3.3 7.4 + - + +
106B HIS* 2.9 31.1 + - + +
147B LEU* 4.1 19.5 - - + -
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.6 0.6 - - - +
100B SER* 4.4 4.8 + - - -
101B PRO 3.2 0.4 - - - -
102B VAL* 1.3 80.4 - - - +
104B GLN* 1.3 60.1 + - - +
106B HIS* 3.4 5.8 + - - +
107B ALA* 3.1 22.1 + - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.8 28.7 - - + +
100B SER 4.2 5.6 + - - +
101B PRO* 3.3 20.8 + - - +
103B GLY* 1.3 71.3 - - - +
105B LEU* 1.3 60.5 + - - +
107B ALA* 3.3 7.1 + - - +
108B SER* 2.9 33.3 + - - +
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Residues in contact with LEU 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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21B LEU* 3.8 21.2 - - + +
24B LEU* 3.5 33.5 - - + +
25B ALA* 3.9 23.3 - - + +
85B LEU* 4.0 5.8 - - + -
101B PRO* 2.8 26.6 + - + +
102B VAL* 3.5 8.7 - - + +
104B GLN* 1.3 74.6 - - - +
106B HIS* 1.3 57.7 + - - +
108B SER* 3.1 3.3 + - - -
109B LEU* 2.9 34.1 + - + +
147B LEU* 4.2 17.9 - - + -
150B LEU* 3.9 26.9 - - + -
154B VAL* 6.3 0.2 - - + -
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 3.2 37.9 + - - -
85B LEU* 3.9 18.5 - - + +
86B GLY* 4.1 11.7 + - - -
102B VAL* 2.9 18.7 + - + +
103B GLY* 3.6 6.5 + - - +
105B LEU* 1.3 75.8 - - - +
107B ALA* 1.4 64.1 + - - +
109B LEU* 3.1 10.1 + - - +
110B LEU* 3.0 60.8 + - + +
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Residues in contact with ALA 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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103B GLY 3.1 10.6 + - - +
104B GLN* 3.6 10.8 - - - +
106B HIS* 1.4 80.3 + - - +
108B SER* 1.4 51.9 + - - +
110B LEU* 3.3 11.5 + - - +
111B GLY* 2.8 31.7 + - - -
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Residues in contact with SER 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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17B LEU* 3.2 21.8 - - - +
20B LYS* 5.6 3.1 - - - +
21B LEU* 3.6 28.5 - - - -
24B LEU* 3.6 14.0 - - - +
104B GLN* 2.9 18.3 + - - +
105B LEU 3.1 0.4 + - - -
107B ALA* 1.4 72.3 - - - +
109B LEU* 1.3 59.0 + - - +
111B GLY* 4.3 1.1 - - - +
112B LEU* 2.9 27.2 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.0 19.3 - - + -
78B LEU* 3.7 33.7 - - + +
81B TYR* 4.0 24.9 - - + -
82B GLU* 4.0 21.8 - - + +
85B LEU* 4.0 22.9 - - + -
105B LEU 2.9 18.6 + - - +
106B HIS* 3.4 6.5 - - - +
108B SER* 1.3 74.1 - - - +
110B LEU* 1.3 58.4 + - - +
112B LEU* 3.6 1.4 + - - +
113B SER* 3.0 30.0 + - - -
150B LEU* 4.2 23.1 - - + -
153B PHE* 5.5 0.2 - - + -
154B VAL* 4.6 1.1 - - + -
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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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82B GLU* 3.4 28.9 - - + -
106B HIS* 3.0 45.5 + - + +
107B ALA* 3.4 12.6 - - - +
109B LEU* 1.3 74.0 - - - +
111B GLY* 1.3 64.9 + - - +
113B SER* 2.7 21.8 + - - +
114B GLN* 3.0 23.9 + - + +
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.0 13.3 - - - +
107B ALA 2.8 16.9 + - - -
108B SER* 3.3 3.5 + - - -
110B LEU* 1.3 77.6 - - - +
112B LEU* 1.3 60.0 + - - +
114B GLN* 3.5 7.3 + - - +
115B LEU* 3.3 18.5 + - - +
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Residues in contact with LEU 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 CYS* 4.0 32.8 - - + +
17B LEU* 3.7 30.5 - - + +
18B SER* 3.2 24.9 - - - +
21B LEU* 3.8 20.6 - - + -
78B LEU* 3.9 23.5 - - + +
108B SER 2.9 16.1 + - - +
109B LEU 4.0 2.9 - - - +
111B GLY* 1.3 71.6 - - - +
113B SER* 1.4 64.8 + - - +
114B GLN 3.1 1.8 - - - -
115B LEU* 3.1 16.0 + - + +
116B LEU* 3.3 12.3 + - + +
157B ALA* 5.3 2.0 - - + -
161B PHE* 4.0 10.8 - - + -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.7 15.0 + - - -
78B LEU* 3.9 17.1 - - - +
79B ILE* 3.5 32.3 - - - +
109B LEU 3.0 16.2 + - - -
110B LEU* 2.7 26.3 + - - +
112B LEU* 1.4 74.0 - - - +
114B GLN* 1.3 61.6 + - - +
116B LEU* 3.2 5.9 + - - +
117B GLN 3.2 19.8 + - - +
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Residues in contact with GLN 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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110B LEU* 3.0 31.9 + - + +
111B GLY* 3.5 7.2 - - - +
112B LEU 3.1 0.2 - - - -
113B SER* 1.3 79.1 - - - +
115B LEU* 1.3 60.9 + - - +
116B LEU 3.1 0.2 - - - -
117B GLN 4.5 3.9 - - - +
118B PRO* 3.1 52.6 - - + +
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Residues in contact with LEU 115 (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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9B PRO* 4.2 12.9 - - - +
10B ALA* 3.9 27.4 - - + -
13B GLN* 4.1 19.7 - - + -
14B CYS* 4.1 23.3 - - - -
17B LEU* 3.6 30.5 - - + -
111B GLY 3.3 6.0 + - - +
112B LEU* 3.1 11.3 + - + +
114B GLN* 1.3 77.2 - - - +
116B LEU* 1.3 60.6 + - - +
118B PRO* 4.3 7.9 - - - +
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Residues in contact with LEU 116 (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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9B PRO* 5.5 9.7 - - - +
14B CYS* 5.7 3.4 - - - -
71B LEU* 5.2 7.2 - - + +
74B ILE* 6.3 1.1 - - + -
75B HIS* 4.4 22.2 - - + -
78B LEU* 5.4 3.6 - - + -
112B LEU 3.3 8.2 + - - +
113B SER* 3.2 11.2 + - - +
114B GLN 3.1 0.8 - - - -
115B LEU* 1.3 81.3 - - - +
117B GLN* 1.3 60.7 + - - +
118B PRO* 3.9 2.1 - - - +
161B PHE* 5.9 7.6 - - + -
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 4.3 27.4 + - + +
113B SER 3.2 9.5 + - - +
114B GLN* 3.4 7.5 - - - +
116B LEU* 1.3 79.2 - - - +
118B PRO* 1.4 69.4 - - - +
119B GLU 3.6 9.9 - - - +
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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