Contacts of the helix formed by residues 15 - 37 (chain B) in PDB entry 1QI9
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 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLY 4.5 0.5 - - - +
39A THR* 3.8 14.8 - - + +
40A VAL 3.7 19.9 + - - +
3B CYS* 3.7 15.0 - - - -
4B SER 3.4 16.4 - - - +
5B THR 3.6 13.7 - - - +
6B SER* 3.7 3.4 - - - +
7B ASP* 3.5 36.8 - - + +
13B THR 3.6 0.4 - - - -
14B PRO* 1.3 83.3 - - + +
16B ASN* 1.3 59.5 + - - +
17B GLU 3.2 0.2 - - - -
18B ARG* 3.3 37.7 + - - +
19B ASP* 4.3 2.9 + - - +
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Residues in contact with ASN 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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39A THR* 3.5 23.7 + - + +
4B SER* 3.1 36.4 + - - +
5B THR* 4.2 7.4 + - - +
14B PRO* 3.1 13.2 - - - +
15B PRO* 1.3 78.9 - - - +
17B GLU* 1.3 70.5 + - - +
19B ASP* 3.2 13.5 - - - +
20B ASP* 4.1 5.5 - - - +
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Residues in contact with GLU 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 THR* 3.7 11.2 - - + +
14B PRO* 2.8 32.5 + - - +
16B ASN* 1.3 90.0 + - - +
18B ARG* 1.3 60.1 + - - +
19B ASP* 3.3 5.6 - - - -
20B ASP* 3.2 15.7 + - + +
21B GLU* 2.9 36.7 + - + +
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Residues in contact with ARG 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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40A VAL 4.1 5.9 + - - -
42A GLN* 3.9 8.9 - - - +
117A ALA* 5.6 1.2 - - - +
118A PHE* 5.9 0.9 - - + -
119A SER* 3.5 31.3 + - - +
339A TYR* 3.4 16.2 + - - -
7B ASP* 2.8 42.0 + - - +
9B ALA* 4.0 1.6 + - - +
11B ASP* 3.4 29.5 + - - +
13B THR* 2.7 37.1 + - + -
14B PRO* 3.3 8.3 - - - +
15B PRO* 3.3 32.2 + - - +
17B GLU* 1.3 76.6 - - - +
19B ASP* 1.3 62.2 + - - +
21B GLU* 4.0 3.3 - - - +
22B ALA* 3.2 23.2 + - - +
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Residues in contact with ASP 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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34A LEU* 3.5 36.3 - - + +
37A THR* 4.2 11.1 - - + +
38A GLY* 3.3 41.8 + - - +
39A THR* 5.1 1.0 + - - -
15B PRO 4.3 1.8 + - - -
16B ASN 3.2 24.8 - - - +
17B GLU* 3.5 2.3 - - - -
18B ARG* 1.3 73.5 - - - +
20B ASP* 1.3 71.9 + - - +
22B ALA* 3.3 6.1 + - - +
23B PHE* 3.1 17.3 + - - +
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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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34A LEU* 3.6 19.7 - - - +
16B ASN 4.1 11.0 - - - +
17B GLU* 3.2 18.0 + - + +
19B ASP* 1.3 91.1 + - - +
21B GLU* 1.3 58.7 + - + +
23B PHE* 3.2 5.6 + - - +
24B ALA* 2.9 29.2 + - - +
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Residues in contact with GLU 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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111A ILE* 3.6 14.5 - - + +
13B THR* 2.9 38.4 + - + +
17B GLU* 2.9 23.4 + - + +
18B ARG* 4.1 5.1 - - - +
20B ASP* 1.3 76.4 - - + +
22B ALA* 1.3 64.1 + - - +
24B ALA* 3.5 7.9 + - - +
25B SER* 3.2 23.2 + - - -
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Residues in contact with ALA 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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111A ILE* 3.8 20.8 - - + +
117A ALA* 3.8 28.0 - - + -
18B ARG 3.2 17.9 + - - +
19B ASP* 3.9 4.7 - - - +
20B ASP 3.2 0.2 - - - -
21B GLU* 1.3 72.6 - - - +
23B PHE* 1.3 66.5 + - - +
25B SER* 3.4 1.6 + - - -
26B ARG* 3.1 41.6 + - - +
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Residues in contact with PHE 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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27A VAL* 4.0 15.3 - - + -
30A ALA* 3.5 27.8 - - + +
31A LYS* 3.6 34.5 - - + -
34A LEU* 3.9 28.9 - - + -
19B ASP 3.1 13.4 + - - +
20B ASP* 3.2 8.7 + - - +
22B ALA* 1.3 77.2 - - - +
24B ALA* 1.3 65.9 + - + +
26B ARG* 3.2 6.3 + - - +
27B VAL* 2.9 49.2 + - + +
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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 ASP 2.9 16.4 + - - +
21B GLU* 3.8 8.3 - - + +
22B ALA 3.3 0.2 - - - -
23B PHE* 1.3 84.3 - - + +
25B SER* 1.3 59.4 + - - +
27B VAL* 3.9 4.7 - - - +
28B ALA* 3.1 23.9 + - - +
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Residues in contact with SER 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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111A ILE* 3.8 36.4 + - - +
21B GLU 3.2 17.0 + - - -
22B ALA 3.4 3.1 + - - -
23B PHE 3.3 0.2 - - - -
24B ALA* 1.3 75.7 - - - +
26B ARG* 1.3 58.0 + - - +
28B ALA* 3.3 6.5 + - - +
29B ALA* 3.0 29.2 + - - +
512B THR* 5.1 6.2 - - - +
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Residues in contact with ARG 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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26A ARG 6.6 0.2 - - - -
30A ALA* 4.0 27.3 + - + +
33A GLU* 3.7 27.9 - - - +
111A ILE* 4.0 8.7 - - + +
112A ASP* 3.0 24.8 + - - +
113A ILE* 3.3 40.1 + - + +
114A SER 4.0 0.4 + - - -
115A GLY 2.9 26.0 + - - -
116A PRO 3.8 0.2 - - - -
117A ALA* 3.3 31.6 - - - +
508A GLN* 5.9 1.1 - - - +
22B ALA* 3.1 30.7 + - - +
23B PHE* 3.8 3.1 - - - +
25B SER* 1.3 75.6 - - - +
27B VAL* 1.3 58.9 + - - +
29B ALA* 3.4 2.9 + - - +
30B ALA* 2.9 30.0 + - - +
113B ILE* 5.2 1.3 - - + -
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Residues in contact with VAL 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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23A PHE* 3.9 17.1 - - + -
27A VAL* 4.4 18.6 - - + +
30A ALA* 5.0 1.8 - - + -
23B PHE* 2.9 54.9 + - + +
24B ALA* 3.9 5.8 - - - +
26B ARG* 1.3 73.0 - - - +
28B ALA* 1.3 61.9 + - - +
30B ALA* 3.3 6.5 + - - +
31B LYS* 2.8 35.8 + - + +
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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 3.1 17.8 + - - +
25B SER* 3.7 6.3 - - - +
26B ARG 3.3 0.2 - - - -
27B VAL* 1.3 79.4 - - - +
29B ALA* 1.3 55.8 + - - +
31B LYS* 3.6 10.7 - - + +
32B ARG* 3.0 27.5 + - - +
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Residues in contact with ALA 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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113A ILE* 3.8 18.8 - - + -
25B SER* 3.0 17.7 + - - +
26B ARG* 3.7 5.8 - - - +
27B VAL 3.2 0.2 - - - -
28B ALA* 1.3 72.4 - - - +
30B ALA* 1.3 66.6 + - - +
32B ARG* 3.3 9.6 + - - +
33B GLU* 3.2 24.3 + - - +
508B GLN* 4.3 19.3 + - + +
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Residues in contact with ALA 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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23A PHE* 3.6 24.9 - - + +
26A ARG* 3.9 37.7 + - + +
27A VAL* 5.0 2.5 - - + +
113A ILE* 4.4 4.4 - - + +
26B ARG 2.9 17.8 + - - +
27B VAL* 3.8 4.7 - - - +
29B ALA* 1.3 75.5 - - - +
31B LYS* 1.3 57.8 + - - +
33B GLU* 3.3 9.0 + - - +
34B LEU* 2.9 22.5 + - - +
508B GLN* 5.6 0.2 - - - +
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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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23A PHE* 3.5 20.8 - - + -
27B VAL* 2.8 22.2 + - + +
28B ALA* 3.6 9.6 - - + +
29B ALA 3.2 0.2 - - - -
30B ALA* 1.3 76.8 - - - +
32B ARG* 1.3 60.2 + - - +
34B LEU* 3.5 6.9 - - + +
35B GLU* 3.0 61.2 + - + +
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Residues in contact with ARG 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 ALA 3.0 16.5 + - - +
29B ALA* 3.7 9.0 - - - +
30B ALA 3.3 0.2 - - - -
31B LYS* 1.3 76.6 - - - +
33B GLU* 1.3 57.2 + - + +
35B GLU* 4.9 1.6 - - - -
36B GLY* 2.9 27.7 + - - -
507B HIS* 3.7 17.8 + - - +
508B GLN* 6.1 0.6 - - - +
511B MET* 3.4 28.3 - - - +
534B ASP 4.8 1.4 + - - -
535B GLY* 3.0 36.8 + - - -
547B LEU* 2.9 55.6 + - + +
548B VAL* 3.9 20.8 - - + +
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Residues in contact with GLU 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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26A ARG* 3.8 23.7 + - - +
29B ALA 3.2 14.5 + - - +
30B ALA* 3.5 8.7 - - - +
32B ARG* 1.3 74.1 - - + +
34B LEU* 1.3 63.2 + - - +
37B THR* 2.7 35.5 + - - +
115B GLY 4.1 9.4 - - - +
116B PRO* 3.5 13.4 - - - +
117B ALA 4.4 2.6 + - - -
504B ARG* 2.9 51.0 + - - +
508B GLN* 4.0 19.5 + - - +
548B VAL* 4.0 10.5 - - - +
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Residues in contact with LEU 34 (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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19A ASP* 3.5 42.2 - - - +
20A ASP* 3.7 19.7 - - - +
23A PHE* 4.1 33.2 - - + -
30B ALA 2.9 14.1 + - - +
31B LYS* 3.3 14.1 + - + +
33B GLU* 1.3 76.2 - - - +
35B GLU* 1.3 70.5 + - + +
37B THR* 3.9 2.2 - - - -
38B GLY* 3.2 22.7 + - - -
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Residues in contact with GLU 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 57.2 + - + +
32B ARG* 5.0 1.0 - - - -
34B LEU* 1.3 86.4 - - + +
36B GLY* 1.3 60.5 + - - +
38B GLY* 4.2 5.4 + - - -
547B LEU* 3.6 22.2 - - + +
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Residues in contact with GLY 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 ARG 2.9 18.6 + - - -
33B GLU 3.9 0.4 - - - -
35B GLU* 1.3 76.0 - - - +
37B THR* 1.3 62.3 + - - +
547B LEU* 3.7 15.7 - - - +
548B VAL* 3.7 30.2 - - - +
550B THR* 4.8 8.1 - - - +
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Residues in contact with THR 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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18A ARG 6.0 0.2 - - - -
19A ASP* 4.2 15.3 - - + +
33B GLU* 2.7 25.8 + - - +
34B LEU 3.9 1.6 - - - -
35B GLU 4.6 0.2 - - - -
36B GLY* 1.3 81.0 - - - +
38B GLY* 1.3 75.0 + - - +
39B THR 3.7 1.9 + - - +
40B VAL* 3.6 22.8 - - + +
120B ALA* 3.8 25.2 - - + +
504B ARG* 3.3 23.1 + - - +
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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