Contacts of the helix formed by residues 32 - 48 (chain D) in PDB entry 3QSV
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 SER 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D ARG* 4.8 0.2 - - - +
31D GLU* 1.3 83.6 + - - +
33D GLU* 1.3 64.4 + - - +
34D THR* 3.5 9.3 + - - -
35D PHE* 3.0 28.4 + - - +
36D ALA* 3.2 20.4 + - - +
87D ARG* 6.0 0.4 - - - +
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Residues in contact with GLU 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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13C ASN* 4.8 12.0 + - - -
14C ASP* 4.8 10.7 - - - +
24D MET* 3.9 16.6 - - + +
27D ARG* 3.6 22.6 - - - +
32D SER* 1.3 71.1 - - - +
34D THR* 1.3 74.3 + - + +
36D ALA* 3.2 4.9 + - - +
37D LYS* 3.0 22.0 + - + +
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Residues in contact with THR 34 (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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32D SER* 3.5 8.6 + - - -
33D GLU* 1.3 84.2 - - + +
35D PHE* 1.3 72.8 + - - +
37D LYS* 2.9 12.1 + - - +
38D ARG* 2.9 38.2 + - - +
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Residues in contact with PHE 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 GLU* 3.6 30.5 - - + -
32D SER* 3.0 19.6 + - - +
34D THR* 1.3 82.4 + - - +
36D ALA* 1.3 67.0 + - - +
38D ARG* 3.1 9.1 + - - +
39D ALA* 2.9 31.4 + - + +
84D VAL* 3.5 37.8 - - + +
85D ALA* 4.2 12.6 - - + -
87D ARG* 3.6 46.0 - - + +
94D ILE* 4.4 23.3 - - + -
98D LEU* 5.2 3.4 - - + -
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Residues in contact with ALA 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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24D MET* 3.9 6.3 - - - -
27D ARG* 3.9 25.6 - - + +
32D SER 3.2 12.2 + - - +
33D GLU 3.4 9.6 - - - +
34D THR 3.1 0.2 - - - -
35D PHE* 1.3 85.8 - - - +
37D LYS* 1.3 58.5 + - - +
39D ALA* 3.2 2.6 + - - +
40D ILE* 2.9 33.7 + - + +
98D LEU* 3.9 24.9 - - + -
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Residues in contact with LYS 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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20D VAL* 4.2 14.4 - - + -
21D HIS* 4.0 25.2 + - + +
24D MET* 3.7 17.9 - - + -
33D GLU* 3.0 13.3 + - + +
34D THR* 2.9 12.6 + - - +
36D ALA* 1.3 74.5 - - - +
38D ARG* 1.3 59.7 + - - +
40D ILE* 3.2 2.3 + - - +
41D GLU* 2.7 64.3 + - - +
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Residues in contact with ARG 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 THR* 2.9 30.4 + - - +
35D PHE* 3.5 7.9 - - - +
37D LYS* 1.3 81.0 - - - +
39D ALA* 1.3 57.9 + - - +
41D GLU* 3.7 16.7 + - - +
42D SER* 3.0 30.8 + - - -
84D VAL* 4.0 12.5 - - + +
85D ALA* 3.9 21.7 - - + +
2006F C 2.6 65.2 + - - -
2007F T 4.1 10.8 + - - +
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Residues in contact with ALA 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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35D PHE* 2.9 27.9 + - + +
36D ALA 3.7 4.0 - - - +
38D ARG* 1.3 77.3 - - - +
40D ILE* 1.3 61.1 + - - +
42D SER* 3.7 1.9 + - - -
43D LEU 3.2 6.4 + - - -
84D VAL* 3.6 26.6 - - + +
94D ILE* 4.5 5.4 - - + -
95D TYR* 2.6 39.7 + - + +
98D LEU* 4.4 8.5 - - + -
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Residues in contact with ILE 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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20D VAL* 3.8 32.5 - - + +
23D LEU* 4.0 27.6 - - + +
24D MET* 4.0 17.0 - - - +
27D ARG* 5.5 1.1 - - + -
36D ALA* 2.9 18.9 + - + +
37D LYS* 3.8 2.7 - - - +
39D ALA* 1.3 76.1 - - - +
41D GLU* 1.3 66.2 + - - +
43D LEU* 3.2 6.0 + - + +
44D VAL* 2.9 31.7 + - + +
95D TYR* 4.6 0.7 - - + -
98D LEU* 3.9 14.1 - - + -
99D TRP* 3.5 36.6 - - + +
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Residues in contact with GLU 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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17D LEU* 5.1 11.0 - - + +
20D VAL* 4.2 27.2 - - + +
21D HIS* 6.0 0.9 - - - -
37D LYS* 2.7 50.8 + - - +
38D ARG* 3.7 22.1 + - - +
40D ILE* 1.3 72.7 - - - +
42D SER* 1.3 61.9 + - - +
44D VAL* 3.5 1.2 + - - +
45D LYS* 3.1 25.8 + - - +
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Residues in contact with SER 42 (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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38D ARG 3.0 17.7 + - - -
39D ALA* 3.7 7.4 - - - -
41D GLU* 1.3 76.9 - - - +
43D LEU* 1.3 62.6 + - - +
45D LYS* 3.5 5.8 + - - +
46D LYS* 2.8 49.0 + - - +
82D LEU* 4.8 5.0 - - - +
83D GLN 5.8 0.2 + - - -
84D VAL* 5.5 5.1 - - - +
95D TYR* 4.0 5.1 + - - -
2007F T 4.5 14.7 + - - -
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Residues in contact with LEU 43 (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 LEU* 6.3 0.2 - - + -
39D ALA 3.2 4.0 + - - +
40D ILE* 3.2 6.3 + - + +
42D SER* 1.3 80.0 + - - +
44D VAL* 1.3 64.7 - - + +
46D LYS* 3.2 14.8 + - - +
47D LEU* 3.4 29.4 - - + +
57D LEU* 3.7 24.9 - - + -
72D VAL* 5.0 2.5 - - + -
74D ILE* 3.9 24.5 - - + -
95D TYR* 3.4 46.0 - - + +
99D TRP* 4.4 10.5 - - + -
128D VAL* 4.2 20.4 - - + -
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Residues in contact with VAL 44 (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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16D CYS* 4.0 36.6 - - + +
19D ILE* 4.4 9.6 - - + -
20D VAL* 4.0 16.8 - - + -
23D LEU* 4.4 15.3 - - + -
40D ILE* 2.9 29.1 + - + +
41D GLU 4.0 3.6 - - - +
43D LEU* 1.3 78.8 - - + +
45D LYS* 1.3 64.5 + - - +
47D LEU* 2.9 19.1 + - - +
48D LYS* 3.3 10.8 + - + +
54D LEU* 4.8 18.7 - - + +
57D LEU* 5.6 2.0 - - + -
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Residues in contact with LYS 45 (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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16D CYS* 6.1 1.3 - - - -
41D GLU 3.1 17.5 + - - +
42D SER* 3.8 6.7 - - - +
43D LEU 3.3 0.2 - - - -
44D VAL* 1.3 78.1 - - - +
46D LYS* 1.3 62.1 + - + +
47D LEU 3.1 1.2 + - - -
48D LYS* 3.2 53.5 + - - +
49D GLU* 5.8 0.5 - - - +
1011E C 4.8 2.9 + - - -
1012E T 3.4 25.3 + - - -
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Residues in contact with LYS 46 (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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42D SER* 2.8 38.4 + - - +
43D LEU* 3.2 11.3 + - - +
44D VAL 3.2 0.6 - - - -
45D LYS* 1.3 78.8 - - + +
47D LEU* 1.3 62.5 - - - +
48D LYS 3.7 0.2 - - - -
49D GLU* 4.9 7.6 + - - +
50D LYS* 4.9 5.7 - - - -
74D ILE* 3.8 41.3 - - + +
75D GLN* 5.2 7.0 - - + +
82D LEU* 3.9 21.1 - - - +
95D TYR* 5.1 1.2 + - - -
2008F A 5.0 7.6 + - - -
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Residues in contact with LEU 47 (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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43D LEU* 3.4 28.7 - - + +
44D VAL* 2.9 9.4 + - - +
46D LYS* 1.3 82.0 - - + +
48D LYS* 1.3 53.4 + - - +
49D GLU 2.7 17.1 + - - -
50D LYS* 3.0 38.6 + - - +
51D LYS 3.8 0.5 + - - -
53D GLU* 4.3 8.1 - - + +
54D LEU* 4.1 26.8 - - + +
57D LEU* 3.9 15.3 - - + -
72D VAL* 3.6 30.5 - - + -
73D THR 3.5 24.7 - - - +
74D ILE* 4.8 2.0 - - + -
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Residues in contact with LYS 48 (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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16D CYS* 4.8 22.0 - - - -
44D VAL 3.3 7.4 + - - +
45D LYS* 3.2 53.4 + - + +
46D LYS 3.7 0.2 - - - -
47D LEU* 1.3 75.4 - - - +
49D GLU* 1.3 79.3 + - + +
51D LYS* 3.1 30.4 - - - +
54D LEU* 4.5 11.7 - - + -
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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
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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