Contacts of the helix formed by residues 10 - 28 (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 ALA 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B SER* 2.9 16.8 + - - +
9B PRO* 1.4 78.2 - - - +
11B TRP* 1.3 64.8 - - - +
12B THR* 3.3 3.6 - - - -
13B GLN* 3.1 27.1 + - + +
14B CYS 3.1 18.0 + - - -
115B LEU* 3.9 20.4 - - + -
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Residues in contact with TRP 11 (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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8B SER* 4.5 8.5 + - - +
9B PRO* 3.4 35.9 - - + +
10B ALA* 1.3 72.7 - - - +
12B THR* 1.3 53.2 + - - +
14B CYS* 3.3 5.7 + - - +
15B GLN* 2.8 35.3 + - - +
63B LEU* 6.1 2.5 - - + -
67B SER* 4.6 12.6 - - - -
71B LEU* 4.1 24.7 - - + -
160B VAL* 3.8 12.3 - - + -
161B PHE* 3.7 36.1 - + - +
164B GLY* 3.6 35.2 - - - -
165B ALA* 3.6 18.2 - - - -
168B LEU* 4.2 35.9 - - + +
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Residues in contact with THR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ALA 3.1 0.5 + - - -
11B TRP* 1.3 76.1 + - - +
13B GLN* 1.3 72.9 + - - +
15B GLN* 3.2 13.4 + - - +
16B GLN* 3.0 41.4 + - - +
165B ALA* 4.6 11.2 - - + -
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Residues in contact with GLN 13 (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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10B ALA* 3.1 30.8 + - + +
12B THR* 1.3 91.2 + - - +
14B CYS* 1.3 57.9 + - - +
16B GLN* 3.4 16.5 + - - +
17B LEU* 3.0 32.1 + - - +
115B LEU* 4.1 19.5 - - + -
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Residues in contact with CYS 14 (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* 3.1 28.7 - - - -
10B ALA 3.1 6.8 + - - +
11B TRP* 3.6 6.5 - - - +
13B GLN* 1.3 73.2 - - - +
15B GLN* 1.3 60.6 + - - +
17B LEU* 3.9 0.9 - - - +
18B SER* 2.9 34.7 + - - -
112B LEU* 4.0 21.4 - - + +
115B LEU* 4.1 21.1 - - - -
116B LEU* 5.4 2.7 - - - -
161B PHE* 3.5 36.3 - - + -
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Residues in contact with GLN 15 (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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291A ARG* 5.4 6.2 - - - +
292A TYR* 5.0 4.9 + - + -
11B TRP 2.8 17.9 + - - +
12B THR* 3.2 14.7 + - - +
14B CYS* 1.3 76.5 - - - +
16B GLN* 1.3 75.9 + - - +
18B SER* 3.9 2.1 - - - -
19B GLN* 3.1 39.3 + - - +
158B ALA* 5.0 2.8 - - - +
161B PHE* 3.7 17.6 - - - +
162B ALA* 3.8 29.2 - - + -
165B ALA* 4.4 5.8 - - + +
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Residues in contact with GLN 16 (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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12B THR* 3.0 33.4 + - + +
13B GLN* 3.8 17.8 + - - +
14B CYS 3.4 0.2 - - - -
15B GLN* 1.3 90.8 - - - +
17B LEU* 1.4 61.2 + - - +
19B GLN* 3.4 5.1 + - - +
20B LYS* 3.2 21.7 + - - +
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Residues in contact with LEU 17 (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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13B GLN 3.0 15.0 + - - +
16B GLN* 1.4 72.9 - - - +
18B SER* 1.3 61.2 + - - +
20B LYS* 3.2 9.7 + - + +
21B LEU* 3.0 26.9 + - + +
108B SER* 3.2 41.7 - - - +
111B GLY* 4.0 6.3 - - - -
112B LEU* 3.7 30.7 - - + +
115B LEU* 3.6 28.3 - - + -
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Residues in contact with SER 18 (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 2.9 15.8 + - - -
15B GLN* 4.0 3.4 - - - -
17B LEU* 1.3 76.2 - - - +
19B GLN* 1.3 60.8 + - - +
21B LEU* 3.4 9.6 + - - +
22B CYS* 3.1 27.0 + - - -
112B LEU* 3.2 18.1 - - - +
154B VAL* 4.6 2.2 - - - +
157B ALA* 4.1 7.1 - - - +
158B ALA* 3.7 26.5 - - - -
161B PHE* 3.1 22.6 - - - -
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Residues in contact with GLN 19 (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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270A ASP* 4.1 13.1 - - - +
291A ARG* 3.4 36.0 + - - +
292A TYR* 3.5 28.1 - - + -
15B GLN* 3.1 32.9 + - - +
16B GLN* 3.6 6.3 - - - +
18B SER* 1.3 73.5 - - - +
20B LYS* 1.4 64.1 + - - +
22B CYS* 3.2 6.3 + - - +
23B THR* 3.1 29.5 + - - -
158B ALA* 4.6 0.2 - - - +
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Residues in contact with LYS 20 (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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16B GLN 3.2 13.3 + - - +
17B LEU* 3.2 11.9 + - + +
19B GLN* 1.4 70.9 - - - +
21B LEU* 1.4 60.3 + - - +
23B THR* 3.2 9.5 + - - -
24B LEU* 2.9 39.5 + - + +
108B SER* 5.6 3.8 - - - +
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Residues in contact with LEU 21 (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* 3.0 13.6 + - + +
18B SER* 3.5 11.0 - - - +
19B GLN 3.2 0.2 - - - -
20B LYS* 1.4 76.0 - - - +
22B CYS* 1.3 55.0 + - - +
24B LEU* 3.4 6.1 + - - +
25B ALA* 3.0 31.0 + - - +
78B LEU* 4.4 1.8 - - + -
105B LEU* 3.8 31.2 - - + +
108B SER* 3.6 37.0 - - - +
109B LEU* 4.0 25.6 - - + -
112B LEU* 3.8 28.5 - - + -
150B LEU* 5.9 0.2 - - + -
154B VAL* 4.2 21.7 - - + +
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Residues in contact with CYS 22 (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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291A ARG 4.8 0.7 - - - +
292A TYR* 3.3 48.0 - - - +
18B SER 3.1 19.7 + - - -
19B GLN* 3.2 13.0 + - - +
21B LEU* 1.3 73.4 - - - +
23B THR* 1.3 63.1 + - - +
25B ALA* 3.3 5.6 + - - +
26B TRP* 3.2 26.3 - - - +
154B VAL* 3.6 35.7 - - - -
158B ALA* 3.7 4.3 - - - -
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Residues in contact with THR 23 (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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19B GLN* 3.1 23.3 + - - -
20B LYS* 3.2 11.3 + - - -
22B CYS* 1.3 76.3 - - - +
24B LEU* 1.3 59.5 + - + +
26B TRP* 3.2 5.6 + - - +
27B SER* 3.0 30.8 + - - -
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Residues in contact with LEU 24 (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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20B LYS* 2.9 23.2 + - + +
21B LEU* 3.7 1.3 - - - +
23B THR* 1.3 78.0 - - + +
25B ALA* 1.3 61.9 + - - +
27B SER* 2.8 25.2 + - - +
101B PRO* 3.7 24.7 - - + +
104B GLN* 3.8 50.3 - - + +
105B LEU* 3.5 19.5 - - + +
108B SER* 3.6 26.9 - - - +
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Residues in contact with ALA 25 (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 3.0 18.8 + - - +
22B CYS 3.7 4.9 - - - +
23B THR 3.3 0.6 - - - -
24B LEU* 1.3 76.3 - - - +
26B TRP* 1.3 57.9 + - + +
28B ALA 4.4 6.9 - - - +
101B PRO* 5.7 0.7 - - - -
105B LEU* 3.9 19.7 - - + +
147B LEU* 5.2 3.4 - - - +
150B LEU* 5.1 5.6 - - + -
151B GLN* 2.9 41.6 + - + +
154B VAL* 4.3 14.4 - - + -
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Residues in contact with TRP 26 (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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292A TYR 3.6 4.9 + - - -
293A TYR* 3.0 72.9 + + - +
294A SER* 3.6 7.9 - - - -
22B CYS* 3.2 24.6 + - - +
23B THR* 3.2 5.1 + - - +
24B LEU 3.1 0.2 - - - -
25B ALA* 1.3 78.5 - - + +
27B SER* 1.3 64.4 + - - +
28B ALA 3.3 5.1 + - - -
148B ARG* 3.5 18.8 - - - -
151B GLN* 3.6 27.3 + - + +
154B VAL* 6.0 0.2 - - - +
27D PRO* 4.2 5.2 - - + +
28D TYR* 3.5 47.4 + + + +
83D MET* 3.8 21.5 - - + -
85D TYR* 3.6 26.2 - - - -
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Residues in contact with SER 27 (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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23B THR* 3.0 20.1 + - - -
24B LEU* 2.8 24.5 + - - +
26B TRP* 1.3 76.7 - - - +
28B ALA* 1.3 58.4 + - - +
101B PRO* 3.6 15.9 - - - +
27D PRO* 3.4 28.1 - - - +
52D LYS* 5.3 3.5 + - - -
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Residues in contact with ALA 28 (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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24B LEU 4.4 1.2 + - - -
25B ALA 4.4 7.6 - - - +
26B TRP 4.3 0.3 - - - +
27B SER* 1.3 79.1 + - - +
29B HIS* 1.3 69.9 + - - +
30B PRO* 3.6 4.7 - - - +
99B ASP* 4.3 12.3 - - + +
100B SER* 5.3 0.2 - - - -
101B PRO* 3.8 30.5 - - + +
27D PRO 4.6 2.5 - - - -
28D TYR* 3.8 15.1 - - - -
52D LYS* 6.0 2.0 - - - +
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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