Contacts of the helix formed by residues 26 - 46 (chain A) in PDB entry 3QIC
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 GLN 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLN* 5.0 15.8 + - + +
25A LEU* 1.3 78.0 - - - +
27A GLU* 1.3 63.1 + - - +
28A GLU* 4.2 7.7 - - + +
29A ASP* 2.8 45.9 + - - +
30A LEU* 3.1 10.1 + - - +
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Residues in contact with GLU 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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25A LEU 3.9 0.2 + - - -
26A GLN* 1.3 73.4 - - - +
28A GLU* 1.3 60.2 + - - +
30A LEU* 3.1 13.5 + - - +
31A LYS* 2.9 57.7 + - + +
429A ARG* 3.9 43.9 + - - +
430A LEU* 4.6 10.2 - - + +
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Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 3.1 6.8 - - + +
27A GLU* 1.3 77.5 - - - +
29A ASP* 1.3 65.4 + - - +
30A LEU 3.2 0.2 - - - -
31A LYS* 4.0 22.7 + - - +
32A LYS* 3.1 24.9 + - - +
35A ARG* 4.1 18.2 + - - +
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN 4.7 1.0 - - - +
25A LEU* 3.7 16.9 - - + +
26A GLN* 2.8 52.0 + - - +
28A GLU* 1.3 78.4 - - - +
30A LEU* 1.3 59.4 + - - +
32A LYS* 3.5 8.7 - - - +
33A VAL* 3.1 31.5 + - - +
269A PHE* 3.8 24.8 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.9 31.6 - - + +
26A GLN 3.1 12.9 + - - +
27A GLU* 3.1 13.6 + - - +
29A ASP* 1.3 79.9 - - - +
31A LYS* 1.3 55.4 + - - +
33A VAL* 3.3 4.2 + - + -
34A MET* 2.7 36.8 + - - +
380A HIS* 3.6 39.7 - - + +
381A MET* 4.3 6.3 - - - +
384A ALA* 3.6 8.5 - - + +
426A SER* 3.6 23.6 - - - +
429A ARG* 4.9 7.2 - - - +
430A LEU* 4.3 20.4 - - + -
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 2.9 44.2 + - + +
28A GLU* 4.0 26.1 + - - +
30A LEU* 1.3 73.5 - - - +
32A LYS* 1.3 59.4 + - - +
34A MET* 3.6 19.7 - - + +
35A ARG* 2.8 51.4 + - - +
429A ARG 5.5 3.4 - - - -
430A LEU* 3.8 18.4 - - + +
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Residues in contact with LYS 32 (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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28A GLU 3.1 20.0 + - - +
29A ASP* 3.5 9.9 - - - +
31A LYS* 1.3 77.0 - - - +
33A VAL* 1.3 62.4 + - - +
35A ARG* 3.3 25.3 + - - +
36A ARG* 3.0 47.4 + - - +
268A GLU* 3.3 23.6 + - - +
269A PHE* 4.7 5.8 - - + -
603A GOL 3.1 37.9 + - - -
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 6.3 0.4 - - + -
29A ASP 3.1 21.1 + - - +
30A LEU* 3.6 9.0 - - + +
32A LYS* 1.3 74.4 - - - +
34A MET* 1.3 64.7 + - - +
36A ARG* 3.3 8.3 + - - +
37A MET* 2.9 24.5 + - + +
260A PHE* 4.2 17.6 - - + -
266A LEU* 4.3 4.9 - - + -
269A PHE* 3.4 31.2 - - + -
289A TYR* 4.7 7.4 - - + -
381A MET* 4.2 26.5 - - + -
384A ALA* 3.8 19.3 - - + -
385A GLY 5.4 0.2 - - - +
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Residues in contact with MET 34 (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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30A LEU 2.7 21.0 + - - +
31A LYS* 3.2 26.0 + - + +
33A VAL* 1.3 75.3 - - - +
35A ARG* 1.3 69.0 + - + +
37A MET* 3.4 4.7 + - - +
38A GLN* 3.1 34.0 + - - +
384A ALA* 3.6 19.9 - - + +
387A ALA* 3.7 16.6 - - - -
388A GLY* 3.5 20.1 - - - -
391A ASN* 3.5 28.5 - - - +
430A LEU* 4.1 13.7 - - + +
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Residues in contact with ARG 35 (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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28A GLU* 4.1 15.0 + - - +
31A LYS* 2.8 41.2 + - - +
32A LYS* 3.6 28.0 - - - +
34A MET* 1.3 82.2 - - + +
36A ARG* 1.3 63.1 + - - +
38A GLN* 3.2 20.0 + - - +
39A LYS* 3.0 21.5 + - - +
603A GOL 2.6 32.4 + - - +
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Residues in contact with ARG 36 (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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32A LYS* 3.0 37.8 + - - +
33A VAL* 3.7 5.5 - - - +
35A ARG* 1.3 74.5 - - - +
37A MET* 1.3 64.6 + - - +
39A LYS* 3.3 10.6 + - + +
40A GLU* 3.1 25.9 + - - +
260A PHE* 3.8 15.0 - - + -
264A GLY 4.6 2.4 + - - -
265A GLU* 2.7 42.5 + - + +
266A LEU* 4.6 1.4 - - - +
267A ASP 5.0 0.4 - - - +
268A GLU* 2.9 35.4 + - - +
269A PHE* 4.4 5.8 - - - -
603A GOL 3.3 44.3 + - - +
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Residues in contact with MET 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 2.9 19.0 + - + +
34A MET* 3.5 8.3 - - - +
36A ARG* 1.3 75.3 - - - +
38A GLN* 1.3 57.1 + - - +
40A GLU* 3.2 3.8 + - - +
41A MET* 3.0 45.1 + - - +
55A VAL* 4.3 6.7 - - - -
257A TRP* 3.9 26.9 - - + -
260A PHE* 3.6 34.2 - - + -
289A TYR* 3.7 38.1 - - + -
384A ALA 5.0 0.4 - - - +
385A GLY* 3.8 24.5 - - - +
388A GLY* 5.2 2.2 - - - -
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Residues in contact with GLN 38 (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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34A MET* 3.1 22.8 + - - +
35A ARG* 3.2 27.7 + - - +
37A MET* 1.3 72.1 - - - +
39A LYS* 1.3 60.8 + - - +
41A MET* 3.3 10.4 + - - +
42A ASP* 3.0 38.4 + - - +
388A GLY* 3.2 37.1 + - - +
391A ASN* 3.8 20.6 - - - +
392A ARG* 3.9 13.8 - - + +
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Residues in contact with LYS 39 (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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35A ARG 3.0 11.3 + - - +
36A ARG* 3.3 13.0 + - + +
38A GLN* 1.3 77.6 - - - +
40A GLU* 1.3 70.1 + - - +
42A ASP* 3.5 11.5 + - + +
43A ARG* 3.1 56.6 + - + +
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Residues in contact with GLU 40 (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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36A ARG 3.1 17.4 + - - +
37A MET 3.7 4.9 - - - +
39A LYS* 1.3 83.7 - - - +
41A MET* 1.3 61.2 + - - +
43A ARG* 2.9 39.6 + - - +
44A GLY 2.9 24.1 + - - -
53A ALA* 4.2 2.3 - - - +
54A SER* 3.4 17.7 + - - +
55A VAL* 3.6 31.2 - - + +
260A PHE* 3.7 11.9 - - + -
263A SER* 5.8 0.3 - - - -
265A GLU* 3.3 30.3 - - + +
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Residues in contact with MET 41 (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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37A MET* 3.0 32.9 + - + +
38A GLN* 3.6 13.2 - - - +
40A GLU* 1.3 76.7 - - - +
42A ASP* 1.3 65.3 + - - +
44A GLY 3.1 9.9 + - - -
45A LEU* 3.1 15.6 + - - +
55A VAL* 4.3 9.0 - - + -
57A MET* 3.5 41.7 - - + +
234A TYR* 4.3 6.5 - - + +
255A THR* 5.1 2.7 - - + -
257A TRP* 6.0 0.2 - - - -
388A GLY 4.5 1.1 - - - -
389A VAL* 3.9 41.7 - - + -
392A ARG* 3.3 35.2 - - + +
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Residues in contact with ASP 42 (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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38A GLN* 3.0 22.7 + - - +
39A LYS* 3.6 11.6 - - + +
41A MET* 1.3 76.7 - - - +
43A ARG* 1.3 63.1 + - - +
45A LEU* 3.3 10.9 + - - +
46A ARG* 3.6 34.6 + - - +
392A ARG* 2.5 37.7 + - - +
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Residues in contact with ARG 43 (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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39A LYS* 3.1 45.8 + - + +
40A GLU* 2.9 33.3 + - - +
41A MET 3.2 0.2 - - - -
42A ASP* 1.3 80.5 - - - +
44A GLY* 1.3 60.3 + - - +
45A LEU 3.5 0.3 + - - -
46A ARG* 3.5 17.0 + - - +
49A THR* 2.7 48.9 + - + +
50A HIS 3.4 1.2 + - - -
52A GLU* 3.2 56.3 + - - +
53A ALA* 3.9 5.8 - - + -
263A SER* 5.8 2.8 + - - -
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Residues in contact with GLY 44 (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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40A GLU 2.9 10.3 + - - -
41A MET 3.1 3.7 + - - -
43A ARG* 1.3 77.8 - - - +
45A LEU* 1.3 59.7 + - - +
46A ARG 3.3 0.7 + - - -
50A HIS* 3.0 27.5 + - - +
53A ALA* 3.5 9.2 - - - +
55A VAL 3.3 23.6 - - - -
56A LYS 3.6 6.2 - - - +
57A MET* 3.8 9.9 - - - +
243A LEU* 4.6 2.1 - - - +
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Residues in contact with LEU 45 (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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41A MET 3.1 12.8 + - - +
42A ASP* 3.7 5.6 - - - +
43A ARG 3.2 0.6 - - - -
44A GLY* 1.3 77.8 - - - +
46A ARG* 1.3 61.2 + - + +
57A MET* 3.9 28.0 - - + +
234A TYR* 3.6 8.1 - - - +
236A GLU* 3.3 14.1 - - + +
240A ASN* 3.7 18.4 - - + +
241A VAL* 4.5 10.5 - - + -
242A GLU* 3.3 26.9 + - - +
243A LEU* 4.0 7.1 - - - +
253A VAL* 4.3 19.1 - - + -
392A ARG* 3.3 38.1 - - - +
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Residues in contact with ARG 46 (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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42A ASP* 3.6 22.6 + - - +
43A ARG* 3.5 25.7 + - - +
44A GLY 3.3 0.6 - - - -
45A LEU* 1.3 82.4 - - + +
47A LEU* 1.3 61.6 + - - +
48A GLU* 3.0 32.4 + - + -
49A THR* 3.3 28.4 + - - +
50A HIS* 2.8 32.8 + - - +
240A ASN 5.9 0.2 - - - +
242A GLU* 3.7 24.7 - - + +
243A LEU* 4.3 0.7 - - - -
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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