Contacts of the helix formed by residues 18 - 35 (chain Q) in PDB entry 6FF7
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 ILE 18 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14Q GLY 4.5 10.8 + - - +
15Q TRP* 3.3 7.5 + - - +
17Q LEU* 1.3 76.9 - - - +
19Q GLU* 1.3 59.4 + - - +
20Q PRO 3.6 1.3 - - - -
21Q THR* 4.0 7.5 - - - -
22Q LEU* 3.0 35.0 + - + +
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Residues in contact with GLU 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q TRP 3.0 17.3 + - - +
16Q GLU* 4.1 11.7 - - - +
17Q LEU 3.5 1.4 - - - -
18Q ILE* 1.3 77.8 - - - +
20Q PRO* 1.4 57.4 - - - +
22Q LEU* 3.9 1.6 - - - +
23Q ASP* 2.9 30.3 + - - +
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Residues in contact with PRO 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Q GLU 4.7 3.4 - - - -
17Q LEU 5.0 1.9 - - - +
18Q ILE 3.6 0.2 - - - -
19Q GLU* 1.4 75.3 - - - +
21Q THR* 1.3 60.5 + - - +
23Q ASP* 3.6 6.6 - - + +
24Q GLU* 2.9 29.5 + - - +
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Residues in contact with THR 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E SER 5.9 3.4 - - - -
17Q LEU 4.8 5.0 + - - -
18Q ILE* 3.6 14.2 + - - +
19Q GLU 3.4 0.4 - - - -
20Q PRO* 1.3 77.8 - - - +
22Q LEU* 1.3 58.3 + - - +
24Q GLU* 3.2 7.7 + - - +
25Q LEU* 2.9 26.6 + - - +
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Residues in contact with LEU 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Q ILE* 3.0 21.4 + - + +
19Q GLU* 4.5 1.8 - - - +
21Q THR* 1.3 73.7 - - - +
23Q ASP* 1.3 58.9 + - - +
25Q LEU* 3.7 8.1 - - - +
26Q ASP* 2.9 28.8 + - - +
83Q TYR* 6.0 6.3 - - + -
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Residues in contact with ASP 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q GLU 2.9 23.2 + - - +
20Q PRO* 3.6 7.2 - - + +
21Q THR 3.2 0.2 - - - -
22Q LEU* 1.3 76.6 - - - +
24Q GLU* 1.3 56.7 + - - +
26Q ASP* 3.3 7.4 + - - +
27Q GLN* 2.9 27.5 + - - +
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Residues in contact with GLU 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Q PRO 2.9 18.3 + - - +
21Q THR* 3.2 6.5 + - - +
23Q ASP* 1.3 72.3 - - - +
25Q LEU* 1.3 60.8 + - - +
27Q GLN* 3.6 6.9 - - - +
28Q LYS* 2.9 29.6 + - - +
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Residues in contact with LEU 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q THR 2.9 15.6 + - - +
22Q LEU* 3.8 9.6 - - - +
23Q ASP 3.3 0.2 - - - -
24Q GLU* 1.3 78.1 - - - +
26Q ASP* 1.3 56.0 + - - +
28Q LYS* 3.5 5.9 + - - +
29Q MET* 2.9 28.4 + - - +
52Q ILE* 5.4 5.8 - - + +
56Q LYS* 5.2 15.3 - - + -
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Residues in contact with ASP 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q LEU 2.9 18.9 + - - +
23Q ASP* 3.6 7.4 - - - +
24Q GLU 3.3 0.2 - - - -
25Q LEU* 1.3 76.0 - - - +
27Q GLN* 1.3 57.9 + - - +
29Q MET* 3.2 7.1 + - - +
30Q ARG* 2.9 27.9 + - - +
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Residues in contact with GLN 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q ASP 2.9 17.2 + - - +
24Q GLU* 3.3 8.7 + - - +
26Q ASP* 1.3 77.7 - - - +
28Q LYS* 1.3 57.3 + - - +
30Q ARG* 3.3 8.5 + - - +
31Q GLU* 2.9 26.3 + - - +
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Residues in contact with LYS 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q GLU 2.9 17.1 + - - +
25Q LEU* 4.0 6.5 - - - +
27Q GLN* 1.3 75.0 - - - +
29Q MET* 1.3 59.1 + - - +
31Q GLU* 3.3 8.7 + - - +
32Q ALA* 2.9 28.4 + - - +
52Q ILE* 5.7 4.4 - - + +
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Residues in contact with MET 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q LEU 2.9 18.5 + - - +
26Q ASP* 3.6 9.0 - - - +
27Q GLN 3.2 0.2 - - - -
28Q LYS* 1.3 75.2 - - - +
30Q ARG* 1.3 58.9 + - - +
32Q ALA* 3.3 7.4 + - - +
33Q GLU* 2.9 29.2 + - - +
49Q ILE* 5.7 5.6 - - + +
52Q ILE* 4.9 14.8 - - + +
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Residues in contact with ARG 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q ASP 2.9 13.9 + - - +
27Q GLN* 3.6 10.8 - - - +
29Q MET* 1.3 76.9 - - - +
31Q GLU* 1.3 56.0 + - - +
33Q GLU* 3.2 7.3 + - - +
34Q THR* 2.9 31.8 + - - -
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Residues in contact with GLU 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Q GLN 2.9 16.7 + - - +
28Q LYS* 3.7 9.6 - - - +
29Q MET 3.3 0.4 - - - -
30Q ARG* 1.3 77.3 - - - +
32Q ALA* 1.3 59.6 + - - +
34Q THR* 3.8 10.7 + - - -
35Q GLU* 4.1 14.0 + - - +
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Residues in contact with ALA 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 6.0 0.3 - - - +
28Q LYS 2.9 16.6 + - - +
29Q MET* 3.3 8.0 + - - +
31Q GLU* 1.3 75.5 - - - +
33Q GLU* 1.3 59.6 + - - +
35Q GLU* 4.9 3.6 + - - +
45Q SER 4.5 11.8 - - - +
48Q PRO* 4.4 31.8 - - + +
49Q ILE* 4.7 11.0 + - - +
52Q ILE* 5.7 2.2 - - + -
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Residues in contact with GLU 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 5.4 15.3 - - + +
67A ARG* 6.5 0.9 - - + -
68A LYS* 5.1 18.0 - - + +
71A ARG* 5.4 6.4 - - - +
179A ALA* 6.4 1.8 - - + -
29Q MET 2.9 16.4 + - - +
30Q ARG* 3.2 8.9 + - - +
32Q ALA* 1.3 79.8 - - - +
34Q THR* 1.3 62.4 + - - +
35Q GLU 3.6 4.7 + - - +
49Q ILE* 5.9 4.9 - - + -
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Residues in contact with THR 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ARG 2.9 17.9 + - - -
31Q GLU* 3.8 7.1 + - - -
32Q ALA 3.6 0.6 - - - -
33Q GLU* 1.3 78.5 - - - +
35Q GLU* 1.3 66.0 + - - +
36Q PRO* 3.8 0.3 - - - +
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Residues in contact with GLU 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q GLU 4.1 11.1 + - - +
32Q ALA* 4.9 3.6 - - - +
33Q GLU 3.6 6.2 - - - +
34Q THR* 1.3 81.4 - - - +
36Q PRO* 1.3 68.9 - - - +
45Q SER* 6.0 1.0 - - - -
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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