Contacts of the helix formed by residues 13 - 30 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 1.3 104.0 - - + +
14A TYR* 1.3 64.9 + - - +
16A SER* 2.9 21.7 + - - +
17A GLN* 3.1 20.1 + - - +
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Residues in contact with TYR 14 (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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12A HIS* 3.0 28.1 + + + +
13A PRO* 1.3 74.9 - - - +
15A TRP* 1.3 84.2 + + + +
17A GLN* 2.9 33.9 + - - +
18A VAL* 3.2 8.5 + - + -
89A ASP* 2.5 35.2 + - + -
216A ASP* 5.5 2.2 - - - -
236A GLN* 4.2 22.3 + - + -
238A PRO* 3.2 35.3 - - + +
241A MET* 3.2 22.0 - - - +
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Residues in contact with TRP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLY* 3.8 17.7 - - - -
9A LYS* 3.5 38.5 - - + +
10A SER* 3.1 36.6 + - - +
11A VAL 4.5 1.1 - - - +
12A HIS* 2.9 21.0 + - + +
14A TYR* 1.3 89.4 - + + +
16A SER* 1.3 59.5 + - - +
17A GLN 3.3 0.2 - - - -
18A VAL* 3.7 34.3 - - + -
19A GLU 3.2 6.4 + - - -
35A PHE* 3.1 27.3 - + + -
37A VAL* 4.2 7.0 - - + -
64A ALA* 3.3 26.2 - - + -
88A LEU* 4.8 5.6 - - + -
89A ASP* 3.4 35.4 - - + -
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Residues in contact with SER 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.1 6.4 + - - +
12A HIS 3.3 8.0 + - - -
13A PRO* 2.9 16.3 + - - +
15A TRP* 1.3 75.8 - - - +
17A GLN* 1.3 61.6 + - - +
18A VAL 3.2 0.4 - - - -
19A GLU* 3.2 20.4 + - - +
20A GLN* 3.0 32.6 + - - +
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Residues in contact with GLN 17 (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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13A PRO* 3.3 17.1 + - + +
14A TYR* 2.9 14.5 + - - +
16A SER* 1.3 77.2 - - - +
18A VAL* 1.3 61.0 + - - +
20A GLN* 3.6 4.4 + - - +
21A GLY 3.4 7.8 + - - -
236A GLN 5.3 0.2 - - - +
238A PRO* 3.8 26.7 - - + +
239A TYR* 3.0 29.3 + - - +
292A TYR* 5.7 0.3 + - - -
296A MET* 5.1 6.4 - - - +
301A ILE* 3.5 46.3 - - + +
302A PRO 5.3 0.2 + - - -
303A ILE* 6.0 3.6 - - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.7 0.4 - - + -
14A TYR* 3.2 9.2 + - + +
15A TRP* 3.7 33.4 - - + +
17A GLN* 1.3 76.4 - - - +
19A GLU* 1.3 67.5 + - - +
21A GLY* 2.9 12.8 + - - -
22A VAL* 2.9 14.2 + - + +
35A PHE* 3.7 18.2 - - + -
88A LEU* 4.0 24.0 - - + -
238A PRO* 3.4 34.8 - - + +
241A MET* 4.7 5.6 - - + -
242A GLY* 4.0 8.9 - - - -
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Residues in contact with GLU 19 (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 TRP 3.2 11.5 + - - +
16A SER* 3.2 26.9 + - - +
18A VAL* 1.3 79.4 - - - +
20A GLN* 1.3 60.3 + - + +
22A VAL* 3.2 5.0 - - - +
23A LYS* 2.9 47.4 + - + +
35A PHE* 3.5 44.4 - - + +
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Residues in contact with GLN 20 (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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16A SER* 3.0 19.5 + - - +
17A GLN* 4.1 3.6 - - - +
18A VAL 3.1 0.2 - - - -
19A GLU* 1.3 76.8 - - + +
21A GLY* 1.3 61.3 + - - +
23A LYS* 3.7 6.8 - - + +
24A ALA* 2.9 30.1 + - - +
239A TYR* 3.4 13.7 - - + -
299A LEU 3.1 26.1 + - - -
300A GLY* 2.8 25.6 + - - +
301A ILE* 4.4 7.8 - - + +
302A PRO* 4.7 4.5 - - - +
123D LYS* 5.5 2.1 - - - +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLN 3.4 1.0 + - - -
18A VAL 2.9 4.6 + - - -
20A GLN* 1.3 72.7 - - - +
22A VAL* 1.3 67.1 + - - +
24A ALA 3.2 0.9 + - - -
25A ALA 3.0 19.6 + - - -
239A TYR* 3.3 47.5 - - - -
243A TYR* 3.4 18.6 - - - -
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 3.8 33.2 - - + -
18A VAL* 2.9 21.3 + - + +
19A GLU* 3.2 9.4 - - - +
21A GLY* 1.3 77.5 - - - +
23A LYS* 1.3 64.7 + - + +
25A ALA* 3.2 4.2 + - - +
26A GLY 3.2 15.8 + - - -
33A THR* 3.5 34.3 - - + +
35A PHE* 4.1 18.8 - - + +
242A GLY* 3.7 17.9 - - - +
243A TYR 3.7 1.6 - - - +
246A VAL* 3.8 14.2 - - + +
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Residues in contact with LYS 23 (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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19A GLU* 2.9 35.5 + - + +
20A GLN* 3.8 8.5 - - + +
22A VAL* 1.3 75.5 - - + +
24A ALA* 1.3 64.8 + - - +
26A GLY* 3.3 2.1 + - - +
27A LYS* 3.2 26.4 + - - +
33A THR* 4.2 20.6 - - - +
35A PHE* 6.3 2.0 - - + -
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Residues in contact with ALA 24 (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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20A GLN 2.9 17.4 + - - +
21A GLY 3.2 1.3 + - - +
23A LYS* 1.3 73.6 - - - +
25A ALA* 1.3 62.3 + - - +
27A LYS* 3.5 6.6 + - - +
28A ALA* 3.2 24.4 + - - +
239A TYR* 2.9 30.3 - - + +
243A TYR* 3.5 13.8 + - + -
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Residues in contact with ALA 25 (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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21A GLY 3.0 10.9 + - - +
22A VAL 3.6 4.0 - - - +
23A LYS 3.2 0.2 - - - -
24A ALA* 1.3 76.9 - - - +
26A GLY* 1.3 63.2 + - - +
28A ALA* 3.4 1.5 + - - +
29A LEU* 3.1 31.9 + - + +
243A TYR* 3.5 43.5 - - + +
246A VAL* 3.5 21.8 - - + -
247A THR* 4.4 4.0 - - - +
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Residues in contact with GLY 26 (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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22A VAL 3.2 10.1 + - - -
23A LYS 3.3 3.7 + - - -
25A ALA* 1.3 73.4 - - - +
27A LYS* 1.3 54.5 + - - +
30A GLY* 2.7 15.6 + - - -
31A VAL* 2.7 55.2 + - - +
33A THR* 4.0 10.5 - - - +
246A VAL* 4.4 0.2 - - - +
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Residues in contact with LYS 27 (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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23A LYS* 3.2 13.8 + - + +
24A ALA* 3.7 9.9 - - - +
25A ALA 3.3 0.2 - - - -
26A GLY* 1.3 76.0 - - - +
28A ALA* 1.3 61.9 + - + +
30A GLY* 3.4 11.1 + - - -
209D LYS* 6.1 2.7 - - - +
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Residues in contact with ALA 28 (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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24A ALA 3.2 14.5 + - - +
25A ALA* 3.4 2.7 + - - +
27A LYS* 1.3 79.9 - - + +
29A LEU* 1.3 65.8 + - + +
243A TYR* 4.1 15.5 - - - +
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Residues in contact with LEU 29 (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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25A ALA* 3.1 20.1 + - - +
28A ALA* 1.3 84.9 - - + +
30A GLY* 1.3 64.2 + - - +
31A VAL* 4.5 4.7 - - + -
243A TYR* 6.4 0.9 - - + -
246A VAL* 4.5 5.8 - - + -
247A THR* 3.8 37.2 - - + +
250A TYR* 3.6 64.8 + - + -
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Residues in contact with GLY 30 (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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1A MET* 3.8 23.4 - - - +
2A LEU* 5.2 1.4 + - - +
26A GLY 2.7 10.8 + - - -
27A LYS* 3.4 9.6 + - - -
28A ALA 3.5 0.2 - - - -
29A LEU* 1.3 82.0 - - - +
31A VAL* 1.3 57.7 + - - +
250A 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