Contacts of the helix formed by residues 22 - 41 (chain D) in PDB entry 3CUQ
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 ASN 22 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B GLU* 3.1 35.7 + - + +
362B LYS* 3.3 18.5 + - - +
363B MET 4.3 0.2 - - - -
364B GLY* 3.4 13.7 - - - +
366B LEU 5.9 0.7 - - - +
20D GLN* 3.3 2.7 - - + +
21D PRO* 1.3 78.9 - - + +
23D VAL* 1.3 52.9 + - - +
24D ASP* 3.0 12.7 + - - +
25D THR* 2.8 37.6 + - - -
26D ARG* 2.7 34.4 + - - +
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PRO 3.5 5.4 + - - +
22D ASN* 1.3 69.4 + - - +
24D ASP* 1.3 76.0 + - - +
26D ARG* 3.5 8.9 + - + +
27D GLN* 3.2 35.4 + - + +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B MET* 3.5 25.2 - - + +
22D ASN* 3.0 10.4 + - - +
23D VAL* 1.3 87.0 - - - +
25D THR* 1.3 62.3 + - - +
27D GLN* 3.3 26.6 + - - +
28D LYS* 3.4 11.1 + - - +
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Residues in contact with THR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B GLY* 4.9 0.2 - - - -
366B LEU 5.6 0.3 + - - -
367B CYS* 4.5 3.6 - - + -
380B ASN* 2.9 39.8 + - - +
382B PHE* 3.9 12.9 - - + +
383B MET* 3.6 10.3 - - - +
20D GLN* 3.2 34.5 - - + +
22D ASN* 2.8 30.0 + - - +
24D ASP* 1.3 70.3 - - - +
26D ARG* 1.3 59.6 + - - +
28D LYS* 3.3 4.3 + - - +
29D GLN* 2.8 26.2 + - - +
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.7 37.9 + - + +
20D GLN* 2.8 34.5 + - - +
21D PRO* 3.6 18.1 + - - +
22D ASN 2.7 15.0 + - - +
23D VAL* 3.8 11.3 - - + +
24D ASP 3.4 0.2 - - - -
25D THR* 1.3 73.4 - - - +
27D GLN* 1.3 53.0 + - - +
29D GLN* 4.0 12.1 - - - +
30D LEU* 2.6 61.1 + - + +
76D ILE* 5.9 3.2 - - - +
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Residues in contact with GLN 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.2 30.8 + - + +
24D ASP* 3.5 22.5 + - - +
25D THR 3.2 0.4 - - - -
26D ARG* 1.3 77.1 - - - +
28D LYS* 1.3 57.1 + - - +
30D LEU* 3.5 11.8 - - + +
31D ALA* 2.7 36.9 + - - +
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B PHE* 3.6 36.6 + - + +
383B MET* 3.7 32.7 - - + +
24D ASP 3.4 3.8 + - - -
25D THR 3.3 7.9 + - - +
27D GLN* 1.3 78.9 - - - +
29D GLN* 1.3 60.7 + - - +
31D ALA* 3.6 7.7 + - + +
32D ALA* 3.0 25.8 + - - +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B PHE* 4.4 17.8 - - + -
15D PRO 3.7 4.0 + - - -
16D PHE* 3.2 25.3 + - + -
18D THR 2.6 32.6 + - - -
19D LEU* 3.4 9.5 - - + +
20D GLN* 2.6 34.6 + - + +
25D THR 2.8 14.0 + - - +
26D ARG* 3.3 12.6 - - - +
28D LYS* 1.3 72.1 - - - +
30D LEU* 1.3 67.8 + - - +
32D ALA* 3.0 6.9 + - - +
33D TRP* 3.0 38.9 + - + +
69D LEU* 6.0 1.2 - - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 5.2 5.8 - - + -
26D ARG* 2.6 50.9 + - + +
27D GLN* 3.5 11.4 - - + +
29D GLN* 1.3 73.5 - - + +
31D ALA* 1.3 61.5 + - - +
33D TRP* 3.4 10.3 + - - +
34D CYS* 3.1 27.6 + - - -
76D ILE* 4.1 20.2 - - + -
77D VAL* 4.5 13.0 - - + +
80D GLU* 3.7 40.6 - - + +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLN 2.7 21.7 + - - +
28D LYS* 3.7 9.2 - - + +
30D LEU* 1.3 73.1 - - - +
32D ALA* 1.3 58.0 + - - +
34D CYS* 2.8 27.5 + - - +
35D SER* 2.9 14.4 + - - -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B PHE* 5.5 0.4 - - + -
8D PRO* 6.0 0.5 - - - +
10D GLN* 3.7 27.6 - - + +
16D PHE* 3.9 18.4 - - + -
28D LYS 3.0 15.6 + - - +
29D GLN* 3.0 4.5 + - - +
31D ALA* 1.3 78.2 - - - +
33D TRP* 1.3 56.0 + - - +
35D SER* 3.6 9.6 + - - -
36D LEU* 3.2 27.7 + - - +
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Residues in contact with TRP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 5.3 0.9 - + - -
16D PHE* 3.0 61.0 + + - -
17D PHE* 3.9 19.3 - + - -
29D GLN* 3.0 26.4 + - + +
30D LEU* 3.5 11.9 - - - +
31D ALA 3.1 0.2 - - - -
32D ALA* 1.3 74.8 - - - +
34D CYS* 1.3 64.4 + - - +
36D LEU* 3.3 21.4 + - + +
37D VAL* 3.1 28.1 + - + +
59D LEU* 3.3 29.6 - - + -
60D PHE* 3.6 26.7 - + - -
69D LEU* 3.7 27.8 - - + +
77D VAL* 3.9 17.3 - - + -
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Residues in contact with CYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 3.1 18.0 + - - -
31D ALA* 2.8 14.2 + - - +
33D TRP* 1.3 70.3 - - - +
35D SER* 1.3 64.8 + - - +
36D LEU 3.0 1.6 + - - -
37D VAL* 3.3 10.2 - - - +
38D LEU* 3.1 28.6 + - - +
77D VAL* 4.4 11.0 - - - -
80D GLU* 4.3 23.1 - - - -
81D LEU* 4.2 19.4 - - + +
84D LYS* 4.4 27.1 - - - -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA 2.9 11.7 + - - -
32D ALA* 3.6 14.1 - - - -
34D CYS* 1.3 77.0 - - - +
36D LEU* 1.3 56.4 + - - +
38D LEU* 3.4 17.1 - - - +
39D SER* 3.0 24.9 + - - -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TRP* 4.4 15.9 - - + -
8D PRO* 3.5 39.9 - - + -
11D TYR* 4.7 10.3 - - + -
16D PHE* 4.9 6.7 - - + -
32D ALA 3.2 15.7 + - - +
33D TRP* 3.3 35.2 + - + +
34D CYS 3.1 0.8 - - - -
35D SER* 1.3 77.4 - - - +
37D VAL* 1.3 56.5 + - - +
39D SER* 3.0 8.1 + - - +
40D PHE* 2.7 39.9 + - + +
59D LEU* 3.9 15.9 - - + +
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 3.1 19.7 + - + +
34D CYS* 3.3 10.5 - - - +
36D LEU* 1.3 77.5 - - - +
38D LEU* 1.3 64.4 + - - +
39D SER 3.4 0.2 + - - -
40D PHE* 3.6 7.1 + - - +
41D CYS* 3.2 30.3 + - - -
59D LEU* 4.2 27.8 - - + -
60D PHE* 5.3 7.4 - - + -
77D VAL* 5.1 2.7 - - + -
78D LEU* 5.9 1.6 - - + -
81D LEU* 3.2 37.9 - - + -
97D PHE* 6.5 0.4 - - + -
99D ILE* 4.5 15.7 - - + -
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Residues in contact with LEU 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D CYS 3.1 16.4 + - - +
35D SER* 3.4 31.6 - - - +
37D VAL* 1.3 79.6 - - + +
39D SER* 1.3 60.2 + - - +
41D CYS* 4.0 2.0 + - - +
81D LEU* 5.2 5.8 - - + -
84D LYS* 6.4 1.8 - - - -
86D ASN* 3.8 20.6 - - - +
99D ILE* 4.9 9.6 - - + -
101D TRP* 3.3 56.8 + - + +
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE* 3.7 26.7 + - - +
35D SER 3.0 21.1 + - - -
36D LEU* 3.0 11.8 + - - +
38D LEU* 1.3 81.0 - - - +
40D PHE* 1.3 62.7 + - - +
41D CYS 3.3 0.6 + - - -
42D ARG* 3.7 15.1 + - - +
101D TRP* 5.1 1.4 + - - +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D PHE 4.6 12.1 - - - +
7D TRP* 3.8 37.7 - + - -
36D LEU* 2.7 24.7 + - + +
37D VAL* 4.1 5.6 - - - +
38D LEU 3.5 0.6 - - - -
39D SER* 1.3 68.9 - - - +
41D CYS* 1.3 56.8 + - - +
42D ARG 2.7 17.1 + - - -
43D LEU* 2.9 51.1 + - + +
44D HIS* 3.7 26.5 + + + -
57D SER* 4.3 11.2 - - - -
58D PRO* 4.5 14.4 - - + -
59D LEU* 3.9 27.4 - - + -
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Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 3.2 26.2 + - - +
38D LEU 4.3 0.7 - - - +
39D SER 3.3 1.6 - - - -
40D PHE* 1.3 78.8 - - - +
42D ARG* 1.3 56.5 + - - +
44D HIS* 5.0 2.2 - - - +
45D LYS* 3.4 28.1 - - - +
46D GLN 3.9 14.4 - - - +
47D SER* 3.9 16.4 + - - +
49D MET* 6.2 2.9 - - - -
99D ILE* 3.9 28.7 - - - -
100D MET 4.5 0.9 - - - +
101D TRP* 4.1 20.6 - - + -
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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
------------------------------------------------------------
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