Contacts of the helix formed by residues 13 - 30 (chain B) in PDB entry 3C6Q
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 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B HIS* 1.3 103.3 - - + +
14B TYR* 1.3 65.1 + - - +
16B SER* 2.9 22.4 + - - +
17B GLN* 3.0 19.4 + - - +
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Residues in contact with TYR 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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12B HIS* 3.0 28.3 + + + +
13B PRO* 1.3 75.0 - - - +
15B TRP* 1.3 82.0 + + + +
17B GLN* 2.9 33.0 + - - +
18B VAL* 3.2 11.0 + - + -
89B ASP* 2.5 34.8 + - + -
216B ASP* 5.5 2.0 - - - -
236B GLN* 4.2 22.5 + - + -
238B PRO* 3.2 36.1 - - + +
241B MET* 3.2 21.7 - - - +
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Residues in contact with TRP 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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8B GLY* 3.8 17.9 - - - -
9B LYS* 3.5 38.9 - - + +
10B SER* 3.1 36.6 + - - +
11B VAL 4.5 1.3 - - - +
12B HIS* 2.9 21.0 + - + +
14B TYR* 1.3 89.8 - + + +
16B SER* 1.3 59.6 + - - +
17B GLN 3.3 0.2 - - - -
18B VAL* 3.7 34.1 - - + -
19B GLU 3.3 6.1 + - - -
35B PHE* 3.0 27.3 - + + -
37B VAL* 4.2 7.2 - - + -
64B ALA* 3.3 26.5 - - + -
88B LEU* 4.8 5.6 - - + -
89B ASP* 3.4 35.2 - - + -
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 4.1 6.6 + - - +
12B HIS 3.3 8.0 + - - -
13B PRO* 2.9 16.8 + - - +
15B TRP* 1.3 76.9 - - - +
17B GLN* 1.3 61.9 + - - +
18B VAL 3.2 0.4 - - - -
19B GLU* 3.2 21.0 + - - +
20B GLN* 3.0 32.4 + - - +
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Residues in contact with GLN 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 PRO* 3.3 16.9 + - + +
14B TYR* 2.9 14.5 + - - +
16B SER* 1.3 77.9 - - - +
18B VAL* 1.3 60.6 - - - +
20B GLN* 3.6 4.6 + - - +
21B GLY 3.4 8.5 + - - -
236B GLN 5.3 0.2 - - - +
238B PRO* 3.8 26.8 - - + +
239B TYR* 3.0 28.6 + - - +
292B TYR* 5.7 0.5 + - - -
296B MET* 5.1 6.1 - - - +
301B ILE* 3.4 47.0 - - + +
302B PRO 5.2 0.4 + - - -
303B ILE* 6.0 3.4 - - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.7 0.9 - - + -
14B TYR* 3.2 9.4 + - + +
15B TRP* 3.7 33.9 - - + +
17B GLN* 1.3 75.4 - - - +
19B GLU* 1.3 67.1 + - - +
21B GLY* 3.0 3.5 + - - -
22B VAL* 2.9 24.1 + - + +
35B PHE* 3.7 18.4 - - + -
88B LEU* 4.0 23.6 - - + -
238B PRO* 3.4 35.4 - - + +
241B MET* 4.7 5.6 - - + -
242B GLY* 4.1 8.2 - - - -
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Residues in contact with GLU 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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15B TRP 3.3 11.9 + - - +
16B SER* 3.2 26.9 + - - +
18B VAL* 1.3 78.9 - - - +
20B GLN* 1.3 59.7 + - + +
22B VAL* 3.1 5.6 - - - +
23B LYS* 2.9 45.0 + - + +
35B PHE* 3.5 44.0 - - + +
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Residues in contact with GLN 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 SER* 3.0 20.1 + - - +
17B GLN* 4.1 2.9 - - - +
18B VAL 3.1 0.2 - - - -
19B GLU* 1.3 77.1 - - + +
21B GLY* 1.3 61.8 + - - +
23B LYS* 3.7 7.2 - - + +
24B ALA* 2.8 30.5 + - - +
239B TYR* 3.5 13.0 - - + -
299B LEU 3.0 26.1 + - - -
300B GLY* 2.8 25.8 + - - +
301B ILE* 4.4 8.5 - - + +
302B PRO* 4.7 4.5 - - - +
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Residues in contact with GLY 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 GLN 3.4 1.6 + - - -
18B VAL 3.0 4.4 + - - -
20B GLN* 1.3 74.1 - - - +
22B VAL* 1.3 67.4 + - - +
24B ALA 3.2 1.2 + - - -
25B ALA 3.0 18.7 + - - -
239B TYR* 3.3 45.8 - - - -
243B TYR* 3.4 19.2 - - - -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.8 32.8 - - + -
18B VAL* 2.9 21.5 + - + +
19B GLU* 3.1 9.6 - - - +
21B GLY* 1.3 76.5 - - - +
23B LYS* 1.3 64.1 + - + +
25B ALA* 3.3 4.0 + - - +
26B GLY 3.2 16.5 + - - -
33B THR* 3.5 34.5 - - + +
35B PHE* 4.1 18.2 - - + +
242B GLY* 3.7 17.9 - - - +
243B TYR 3.7 1.6 - - - +
246B VAL* 3.8 13.8 - - + +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 2.9 35.3 + - + +
20B GLN* 3.8 9.0 - - + +
21B GLY 3.2 0.4 - - - -
22B VAL* 1.3 74.1 - - + +
24B ALA* 1.3 65.9 + - - +
26B GLY* 3.3 1.8 + - - +
27B LYS* 3.2 26.8 + - - +
33B THR* 4.3 20.6 - - - +
35B PHE* 6.3 2.0 - - + -
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Residues in contact with ALA 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 GLN 2.8 14.7 + - - +
21B GLY 3.2 1.1 + - - +
23B LYS* 1.3 77.2 - - - +
25B ALA* 1.3 62.2 + - - +
27B LYS* 3.5 6.6 + - - +
28B ALA* 3.2 24.1 + - - +
239B TYR* 2.9 29.8 - - + +
243B TYR* 3.5 13.9 + - + -
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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 GLY 3.0 14.6 + - - +
22B VAL 3.6 0.7 - - - +
23B LYS 3.2 0.2 - - - -
24B ALA* 1.3 77.7 - - - +
26B GLY* 1.3 61.0 + - - +
28B ALA* 3.4 1.5 + - - +
29B LEU* 3.1 32.2 + - + +
243B TYR* 3.5 43.9 - - + +
246B VAL* 3.6 22.0 - - + -
247B THR* 4.4 4.0 - - - +
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Residues in contact with GLY 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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22B VAL 3.2 10.5 + - - -
23B LYS 3.3 3.9 + - - -
25B ALA* 1.3 73.0 - - - +
27B LYS* 1.3 56.3 + - - +
30B GLY* 2.8 13.9 + - - -
31B VAL* 2.7 54.9 + - - +
33B THR* 4.0 10.5 - - - +
246B VAL* 4.4 0.2 - - - +
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Residues in contact with LYS 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 LYS* 3.2 14.0 + - + +
24B ALA* 3.7 9.2 - - - +
25B ALA 3.3 0.2 - - - -
26B GLY* 1.3 74.8 - - - +
28B ALA* 1.3 63.9 + - + +
30B GLY* 3.3 11.3 + - - -
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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 ALA 3.2 14.7 + - - +
25B ALA 3.4 2.2 + - - +
26B GLY 3.3 0.2 - - - -
27B LYS* 1.3 80.0 - - + +
29B LEU* 1.3 59.2 + - - +
243B TYR* 4.1 14.1 - - - +
254C LYS* 3.2 47.1 + - - +
255C ILE* 4.5 3.4 - - + -
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Residues in contact with LEU 29 (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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25B ALA 3.1 19.9 + - - +
28B ALA* 1.3 77.3 - - - +
30B GLY* 1.3 64.0 + - - +
31B VAL* 4.5 4.7 - - + -
246B VAL* 4.5 5.8 - - + -
247B THR* 3.7 30.3 - - - +
250B TYR* 3.6 64.3 + - + -
250C TYR* 5.3 1.5 + - + +
251C LEU* 4.6 10.5 - - + -
254C LYS* 4.0 21.3 - - + +
255C ILE* 3.7 25.1 - - + -
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Residues in contact with GLY 30 (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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1B MET* 3.8 23.4 - - - +
2B LEU* 5.2 1.4 + - - +
26B GLY 2.8 11.0 + - - -
27B LYS* 3.3 9.6 + - - -
28B ALA 3.5 0.2 - - - -
29B LEU* 1.3 82.2 - - - +
31B VAL* 1.3 58.2 + - - +
250B TYR* 5.6 0.9 - - - -
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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