Contacts of the helix formed by residues 16 - 39 (chain B) in PDB entry 4QI1
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 GLU 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY* 3.5 0.5 - - - -
13B VAL* 2.8 23.7 + - - +
14B GLU* 2.8 33.6 + - - +
15B GLY* 1.3 68.2 - - - +
17B GLY* 1.3 65.8 + - - +
18B ILE 3.0 3.4 - - - -
19B TRP* 3.1 20.4 + - - +
20B LEU* 3.3 11.4 + - + +
87B TYR* 2.6 37.1 + - + +
209B LEU* 3.7 12.1 - - + +
210B TYR* 3.9 20.9 - - - -
213B THR* 3.6 31.2 - - + +
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 2.9 31.3 + - - -
12B GLY* 4.3 2.9 - - - -
16B GLU* 1.3 81.9 - - - +
18B ILE* 1.3 57.0 + - - +
19B TRP 3.3 0.2 - - - -
20B LEU* 3.3 16.1 + - - +
21B ALA* 3.0 25.3 + - - +
68B PHE* 3.6 15.5 - - - -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.1 20.0 - - + +
15B GLY 3.2 19.1 + - - +
17B GLY* 1.3 77.7 - - - +
19B TRP* 1.3 84.9 + - + +
21B ALA* 3.3 8.4 + - + +
22B LEU* 3.0 50.9 + - + +
210B TYR* 4.0 9.4 - - + +
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Residues in contact with TRP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.1 16.9 + - - +
18B ILE* 1.3 84.9 - - + +
20B LEU* 1.3 60.0 + - - +
22B LEU* 4.0 22.4 - - + -
23B GLY* 2.9 23.9 + - - -
64B TYR* 4.1 1.2 - - - -
210B TYR* 3.2 69.3 + + - -
213B THR* 4.0 17.7 - - + +
214B LEU* 3.6 43.2 - - + +
217B MET* 3.4 29.9 - - + +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 6.1 0.2 - - - -
16B GLU* 3.6 9.2 - - + +
17B GLY* 3.6 15.7 - - - +
18B ILE 3.3 0.4 - - - -
19B TRP* 1.3 75.7 - - - +
21B ALA* 1.3 53.8 + - - +
24B THR* 2.7 37.2 + - - -
64B TYR* 3.7 27.2 - - + +
67B MET* 3.6 43.1 - - + +
68B PHE* 3.8 17.3 - - + +
87B TYR* 3.7 26.9 - - + +
90B ARG* 4.2 7.6 - - - +
213B THR* 3.8 19.1 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 3.0 16.5 + - - +
18B ILE* 3.3 12.3 + - + +
20B LEU* 1.3 71.6 - - - +
22B LEU* 1.3 62.1 + - + +
24B THR* 3.3 7.0 + - - -
25B ILE* 3.0 41.9 + - + +
68B PHE* 4.0 21.9 - - + -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.0 42.5 + - + +
19B TRP* 4.0 19.3 - - + -
21B ALA* 1.3 73.7 - - + +
23B GLY* 1.3 57.2 + - - +
25B ILE* 3.3 15.5 + - + +
26B GLY* 2.8 32.6 + - - -
217B MET* 4.0 15.7 - - + -
221B LEU* 5.0 3.1 - - - +
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Residues in contact with GLY 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 TRP 2.9 19.1 + - - -
22B LEU* 1.3 75.7 - - - +
24B THR* 1.4 55.8 + - - +
26B GLY* 3.4 0.7 + - - -
27B MET* 2.9 37.2 + - - +
64B TYR* 3.9 17.5 - - - -
217B MET* 3.8 16.4 - - - -
221B LEU* 4.1 7.5 - - - +
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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 LEU 2.7 21.1 + - - -
21B ALA* 3.5 10.3 - - - -
22B LEU 3.3 0.2 - - - -
23B GLY* 1.4 74.3 - - - +
25B ILE* 1.3 60.6 + - + +
27B MET* 3.7 1.9 - - - +
28B LEU* 2.9 29.5 + - + +
61B ALA* 3.7 14.6 - - - +
64B TYR* 3.3 17.8 + - - +
65B LEU* 3.3 26.2 + - + +
68B PHE* 4.8 0.7 - - - +
306B MPG 3.4 30.7 - - + -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.0 27.4 + - + +
22B LEU* 3.8 16.2 - - + +
24B THR* 1.3 78.4 - - + +
26B GLY* 1.3 59.5 + - - +
28B LEU* 3.3 12.2 + - + +
29B LEU* 2.8 51.2 + - + +
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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
----------------------------------------------------------
22B LEU 2.8 17.4 + - - -
23B GLY 3.8 0.7 - - - -
25B ILE* 1.3 74.7 - - - +
27B MET* 1.3 57.7 + - - +
29B LEU* 3.4 7.9 + - - +
30B GLY* 3.0 25.5 + - - -
221B LEU* 3.8 19.3 - - - -
225B VAL* 4.0 5.9 - - - +
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Residues in contact with MET 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 2.9 24.7 + - - +
24B THR 3.7 0.2 - - - +
26B GLY* 1.3 71.6 - - - +
28B LEU* 1.3 58.6 + - - +
30B GLY* 3.3 0.9 + - - -
31B MET* 2.9 30.0 + - - +
57B PRO* 3.6 15.6 - - - +
60B ALA* 3.7 32.3 - - + +
61B ALA* 3.7 23.8 - - + +
64B TYR* 4.7 7.9 - - + -
220B ASP* 3.5 43.7 - - + +
221B LEU* 3.8 10.7 - - + +
224B LYS* 3.9 11.4 - - + -
225B VAL* 4.0 19.3 - - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 2.9 17.4 + - + +
25B ILE* 3.7 11.7 - - + +
27B MET* 1.3 75.9 - - - +
29B LEU* 1.3 60.7 + - + +
31B MET* 3.3 27.1 + - + +
32B LEU* 2.9 52.3 + - + +
61B ALA* 4.1 9.4 - - + +
306B MPG 4.3 29.4 - - + -
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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 ILE* 2.8 39.8 + - + +
26B GLY* 3.8 7.2 - - - +
28B LEU* 1.3 76.3 - - + +
30B GLY* 1.3 64.5 + - - +
32B LEU* 3.4 15.6 + - + +
33B TYR* 3.0 24.3 + - - +
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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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26B GLY 3.0 14.7 + - - -
27B MET 3.7 2.5 - - - -
29B LEU* 1.3 76.4 - - - +
31B MET* 1.3 62.4 - - - +
33B TYR* 3.2 6.9 + - - +
34B PHE* 3.0 35.9 + - - -
225B VAL* 3.9 26.7 - - - -
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Residues in contact with MET 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 MET 2.9 13.2 + - - +
28B LEU* 3.4 31.4 - - + +
30B GLY* 1.3 74.8 - - - +
32B LEU* 1.3 75.3 + - + +
34B PHE* 3.3 6.3 + - - +
35B ILE* 3.0 43.5 + - + +
54B ILE* 3.7 28.9 - - + +
57B PRO* 4.0 17.2 - - + +
58B ALA* 3.5 22.4 - - - +
61B ALA* 5.9 0.4 - - - -
306B MPG 3.5 38.1 - - + -
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Residues in contact with LEU 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 LEU* 2.9 41.0 + - + +
29B LEU* 3.8 16.2 - - + +
30B GLY 3.2 0.4 - - - -
31B MET* 1.3 90.7 - - + +
33B TYR* 1.3 61.5 + - - +
35B ILE* 3.3 12.2 + - + +
36B ALA* 2.9 31.4 + - - +
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Residues in contact with TYR 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 LEU 3.0 16.6 + - - +
30B GLY* 3.2 6.5 + - - +
32B LEU* 1.3 77.8 - - - +
34B PHE* 1.3 76.4 + + - +
36B ALA* 3.3 5.6 + - + +
37B ASP* 2.9 53.9 + - + +
229B PHE* 4.0 33.8 - + - -
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Residues in contact with PHE 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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30B GLY 3.0 24.5 + - - +
31B MET* 3.7 4.5 - - - +
33B TYR* 1.3 96.7 - + + +
35B ILE* 1.3 60.7 + - - +
37B ASP* 3.4 4.5 + - + -
38B GLY 3.1 17.7 + - - -
50B TYR* 3.5 12.6 - - - -
53B THR* 3.6 32.5 - - + -
54B ILE* 3.8 16.6 - - + -
57B PRO* 4.1 13.0 - - + -
224B LYS 4.5 0.9 - - - -
225B VAL* 3.5 28.0 - - + -
228B GLY* 3.7 5.6 - - - -
229B PHE* 3.4 39.5 - - + -
232B LEU* 3.6 19.5 - - + -
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Residues in contact with ILE 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 MET* 3.0 51.8 + - + +
32B LEU* 3.3 13.7 + - + +
34B PHE* 1.3 75.3 - - - +
36B ALA* 1.3 64.1 + - - +
38B GLY* 3.2 10.7 + - - -
39B LEU* 3.4 20.2 + - + +
54B ILE* 3.8 29.2 - - + -
306B MPG 4.1 27.9 - - + +
155C PHE* 5.6 15.5 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.7 + - - +
33B TYR* 3.9 6.3 - - + +
35B ILE* 1.3 78.9 - - + +
37B ASP* 1.3 62.0 + - - +
38B GLY 3.3 0.3 + - - -
39B LEU* 3.4 28.4 + - + +
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Residues in contact with ASP 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 TYR* 2.9 43.0 + - + +
34B PHE* 3.6 8.3 - - + +
36B ALA* 1.3 78.1 - - - +
38B GLY* 1.3 57.4 + - - +
39B LEU 3.4 0.4 + - - -
40B ASP 4.9 1.7 + - - -
41B VAL* 4.4 4.5 - - - +
50B TYR* 2.6 30.9 + - + +
232B LEU* 4.4 10.3 - - + +
233B ARG* 5.7 0.7 - - - -
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Residues in contact with GLY 38 (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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34B PHE 3.1 9.5 + - - -
35B ILE 3.2 3.0 + - - -
37B ASP* 1.3 76.2 - - - +
39B LEU* 1.3 64.9 + - - +
40B ASP 3.3 2.9 - - - -
41B VAL* 3.1 25.9 + - - +
50B TYR* 3.4 25.6 - - - -
306B MPG 3.6 19.0 + - - -
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Residues in contact with LEU 39 (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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35B ILE* 3.4 21.7 + - + +
36B ALA* 3.4 21.5 + - + +
37B ASP 3.4 0.6 - - - -
38B GLY* 1.3 77.5 - - - +
40B ASP* 1.3 69.9 + - - +
41B VAL 3.5 1.6 + - - +
306B MPG 3.6 23.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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