Contacts of the helix formed by residues 18 - 37 (chain B) in PDB entry 6QPA
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 LYS 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.3 18.2 + - + -
17B ASN* 1.3 77.7 + - - +
19B PRO* 1.3 77.5 - - + +
20B ASP* 3.3 29.5 + - + +
21B SER* 3.0 28.5 + - - +
22B TYR* 3.4 15.5 - - - -
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Residues in contact with PRO 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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18B LYS* 1.3 87.4 - - + +
20B ASP* 1.3 66.7 + - - +
21B SER 3.2 0.3 + - - -
22B TYR* 3.3 14.0 + - + +
23B GLU* 3.2 19.4 + - - +
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Residues in contact with ASP 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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18B LYS* 3.1 30.1 + - + -
19B PRO* 1.3 81.1 - - - +
21B SER* 1.3 57.6 + - - +
23B GLU* 3.2 7.2 + - - +
24B THR* 2.9 39.4 + - + +
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Residues in contact with SER 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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15B ILE* 4.6 7.0 - - - -
16B ALA* 2.6 32.4 + - - +
18B LYS* 3.0 16.6 + - - +
20B ASP* 1.3 76.1 - - - +
22B TYR* 1.3 66.2 + - - +
24B THR* 3.4 2.9 + - - -
25B MET* 3.0 29.8 + - - +
109B MET* 3.5 35.4 - - - +
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Residues in contact with TYR 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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17B ASN* 3.3 26.1 + - - -
18B LYS* 3.4 22.0 - - - -
19B PRO* 3.3 9.9 + - + +
21B SER* 1.3 77.8 - - - +
23B GLU* 1.3 62.5 + - - +
25B MET* 3.4 21.3 + - + +
26B MET* 3.1 36.1 + - + +
49B LEU* 3.6 22.8 - - + +
68B ARG* 4.8 4.3 + - - +
74B MET* 3.6 22.0 - - - +
302B MET* 5.3 8.3 - - + -
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Residues in contact with GLU 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 PRO 3.2 11.9 + - - +
20B ASP* 3.5 11.4 - - - +
21B SER 3.2 0.2 - - - -
22B TYR* 1.3 77.9 - - - +
24B THR* 1.3 65.6 + - + +
26B MET* 3.1 27.8 + - - +
27B LYS* 3.0 27.2 + - + +
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Residues in contact with THR 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 ASP* 2.9 21.3 + - + +
21B SER* 3.4 1.3 + - - -
23B GLU* 1.3 78.0 - - + +
25B MET* 1.3 58.2 + - - +
27B LYS* 4.2 10.5 - - - +
28B VAL* 2.9 40.6 + - - +
105B GLY 5.2 10.1 - - - +
106B CYS* 5.0 4.9 - - - -
109B MET* 3.2 32.3 - - + +
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Residues in contact with MET 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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15B ILE* 4.0 22.2 - - + -
21B SER* 3.0 16.0 + - - +
22B TYR* 3.6 44.2 - - + +
23B GLU 3.2 0.2 - - - -
24B THR* 1.3 79.8 + - - +
26B MET* 1.3 58.0 + - + +
29B GLY* 3.2 28.0 + - - +
30B PRO* 3.6 2.6 - - - +
47B GLN* 4.5 18.3 + - - +
49B LEU* 4.5 12.1 - - + -
74B MET* 6.3 0.2 - - - -
76B MET* 4.1 23.1 - - + +
106B CYS* 6.1 0.9 - - - -
109B MET* 3.8 19.5 - - + -
302B MET* 5.8 5.6 - - + -
303B MET* 5.2 1.7 - - - +
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Residues in contact with MET 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 TYR* 3.1 21.9 + - + +
23B GLU* 3.1 33.7 + - - +
25B MET* 1.3 77.4 - - + +
27B LYS* 1.3 57.7 + - - +
30B PRO* 3.5 21.5 - - - +
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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 GLU* 3.0 20.9 + - + +
24B THR* 3.8 9.7 - - - +
26B MET* 1.3 78.4 - - - +
28B VAL* 1.3 70.6 + - + +
30B PRO* 4.4 2.4 - - - +
31B LYS* 3.7 28.2 + - - +
105B GLY* 6.2 1.2 - - - -
224C LEU* 4.2 31.1 - - + +
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Residues in contact with VAL 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 THR* 2.9 24.4 + - - +
27B LYS* 1.3 97.7 - - + +
29B GLY* 1.3 67.2 + - - +
30B PRO 3.4 0.9 - - - -
31B LYS* 2.9 18.0 + - - +
32B VAL* 3.0 15.8 + - + +
102B LEU* 3.4 46.7 - - + +
105B GLY* 5.2 3.8 - - - -
106B CYS* 3.6 24.0 - - - +
224C LEU* 4.7 11.0 - - + -
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Residues in contact with GLY 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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24B THR 4.0 0.8 + - - -
25B MET* 3.2 16.7 + - - +
28B VAL* 1.3 76.2 - - - +
30B PRO* 1.3 69.8 - - - +
32B VAL* 3.1 16.8 + - - +
33B CSS 3.1 17.4 + - - -
47B GLN* 4.8 6.3 - - - -
78B GLN* 6.3 0.9 - - - -
106B CYS* 5.5 0.6 - - - -
303B MET* 4.2 12.1 - - - -
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Residues in contact with PRO 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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25B MET 3.6 5.8 - - - +
26B MET* 3.5 26.2 - - - +
27B LYS 4.4 1.3 - - - +
28B VAL 3.8 2.2 - - - +
29B GLY* 1.3 87.9 - - - +
31B LYS* 1.3 59.0 + - + +
33B CSS 3.2 9.2 + - + +
34B ILE* 3.0 40.9 + - + +
303B MET* 4.3 20.6 - - + -
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Residues in contact with LYS 31 (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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27B LYS* 3.7 22.8 + - - +
28B VAL 2.9 8.5 + - - +
30B PRO* 1.3 78.1 - - + +
32B VAL* 1.3 60.0 + - - +
34B ILE* 3.3 7.5 + - + +
35B THR* 3.0 29.5 + - - +
102B LEU* 3.9 18.4 - - + -
221C VAL* 3.0 39.2 - - + +
222C SER* 4.4 0.7 - - - -
223C THR 3.5 18.6 - - - +
224C LEU* 3.7 26.8 - - + +
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Residues in contact with VAL 32 (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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28B VAL* 3.0 29.5 + - + +
29B GLY* 3.1 8.2 + - - +
31B LYS* 1.3 77.2 - - - +
33B CSS 1.3 65.2 + - - +
35B THR* 3.3 7.0 + - - +
36B THR* 2.9 34.8 + - - +
78B GLN* 4.9 14.6 - - - +
99B ILE* 5.3 11.4 - - + -
102B LEU* 4.0 18.8 - - + -
103B CSS 4.1 23.6 - - - -
106B CYS* 5.5 0.2 - - - -
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Residues in contact with CSS 33 (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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29B GLY 3.1 13.5 + - - -
30B PRO* 3.6 9.4 - - + +
32B VAL* 1.3 79.1 + - - +
34B ILE* 1.3 58.9 + - + +
36B THR* 3.3 9.6 + - - -
37B ALA* 2.9 29.8 + - - +
42B PHE* 4.9 4.1 - - - -
45B PHE* 3.8 59.0 - - + -
78B GLN* 4.7 17.3 - - - -
80B THR* 4.5 13.9 - - - -
303B MET* 4.4 10.1 - - - -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B PRO* 3.0 30.7 + - + +
31B LYS* 3.6 11.2 - - + +
32B VAL 3.2 0.4 - - - -
33B CSS 1.3 75.0 + - + -
35B THR* 1.3 65.7 + - - +
37B ALA* 3.3 13.8 + - - +
38B SER* 3.6 8.8 + - - -
218C MET* 4.1 24.9 - - + +
221C VAL* 3.9 24.7 - - + +
222C SER* 3.6 17.7 - - - +
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Residues in contact with THR 35 (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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31B LYS 3.0 18.8 + - - +
32B VAL 3.3 6.1 + - - +
34B ILE* 1.3 74.2 - - - +
36B THR* 1.3 62.9 + - - +
38B SER* 2.5 30.5 + - - -
91B MET* 4.6 1.1 - - - -
95B ASN* 3.8 20.4 + - - +
98B GLU* 4.8 4.7 - - + -
99B ILE* 3.5 25.7 - - + +
102B LEU* 3.6 18.4 - - + -
219C LYS* 4.7 5.4 - - - +
222C SER* 3.5 29.4 - - - +
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Residues in contact with THR 36 (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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32B VAL* 2.9 24.2 + - - +
33B CSS 3.6 11.2 - - - -
34B ILE 3.3 0.2 - - - -
35B THR* 1.3 78.5 + - - +
37B ALA* 1.3 58.9 + - - +
38B SER 3.0 5.4 + - - -
39B HIS* 3.3 9.9 + - - +
42B PHE* 3.4 40.8 - - + +
80B THR* 4.4 8.4 - - + +
82B TRP* 3.5 19.7 - - + -
91B MET* 3.7 27.3 - - + +
99B ILE* 5.2 1.2 - - - +
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Residues in contact with ALA 37 (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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33B CSS 2.9 16.6 + - - +
34B ILE* 3.3 8.5 + - - +
35B THR 3.2 0.6 - - - -
36B THR* 1.3 74.2 - - - +
38B SER* 1.3 60.4 + - - +
39B HIS 3.2 5.0 + - - +
42B PHE* 3.7 25.5 - - + -
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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