Contacts of the helix formed by residues 32 - 48 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ARG* 4.0 0.4 - - - +
31B GLU* 1.3 82.1 - - - +
33B GLU* 1.3 67.6 + - - +
34B THR* 3.2 11.8 + - - -
35B PHE* 3.3 22.2 + - - +
36B ALA* 3.3 18.2 + - - +
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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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24B MET* 3.7 17.9 - - + +
27B ARG* 3.2 35.7 + - - +
32B SER* 1.3 74.0 - - - +
34B THR* 1.3 65.9 + - + +
36B ALA* 3.9 0.3 - - - +
37B LYS* 3.1 26.1 + - + +
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Residues in contact with THR 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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32B SER* 3.4 13.9 + - - -
33B GLU* 1.3 79.6 - - + +
35B PHE* 1.3 64.2 + - - +
37B LYS* 3.4 11.9 + - + +
38B ARG* 3.0 24.1 + - - +
85B ALA* 6.1 0.7 - - - -
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Residues in contact with PHE 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 GLU* 3.5 27.1 - - + -
32B SER* 3.3 20.0 + - - +
34B THR* 1.3 77.9 - - - +
36B ALA* 1.3 57.6 + - - +
38B ARG* 2.9 7.5 + - - +
39B ALA* 2.7 40.4 + - + +
84B VAL* 3.4 50.5 - - + -
85B ALA* 4.4 10.1 - - + -
87B ARG* 3.4 48.7 - - + +
94B ILE* 4.5 21.3 - - + -
98B LEU* 4.8 2.7 - - + -
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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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24B MET* 3.8 5.8 - - - -
27B ARG* 3.9 29.8 - - + +
31B GLU 5.3 1.1 - - - +
32B SER 3.3 13.6 + - - +
33B GLU 3.9 3.1 - - - +
35B PHE* 1.3 80.1 - - - +
37B LYS* 1.3 57.8 + - - +
39B ALA* 3.3 0.6 + - - +
40B ILE* 2.8 37.1 + - + +
98B LEU* 4.0 29.6 - - + -
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Residues in contact with LYS 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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20B VAL* 4.3 12.8 - - + +
21B HIS* 6.3 0.6 - - - +
24B MET* 3.5 20.7 - - + +
33B GLU* 3.1 21.1 + - + +
34B THR* 3.6 14.1 - - + +
35B PHE 3.2 0.2 - - - -
36B ALA* 1.3 74.4 - - - +
38B ARG* 1.3 58.8 + - - +
40B ILE* 3.8 1.5 - - - +
41B GLU* 2.8 61.7 + - + +
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Residues in contact with ARG 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 THR 3.0 13.1 + - - +
35B PHE 2.9 7.8 + - - +
37B LYS* 1.3 74.5 - - - +
39B ALA* 1.3 58.3 + - - +
41B GLU* 3.2 22.7 + - - +
42B SER* 2.7 57.3 + - - +
45B LYS* 5.9 4.6 - - - +
84B VAL* 3.9 16.2 - - + -
85B ALA* 4.0 21.5 - - + +
1006G C 3.7 19.7 + - - -
1007G T 2.6 34.5 + - - +
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Residues in contact with ALA 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 PHE* 2.7 22.4 + - + +
36B ALA* 3.7 4.3 - - - +
38B ARG* 1.3 73.0 - - - +
40B ILE* 1.3 61.8 + - - +
42B SER* 3.3 3.3 - - - -
43B LEU 3.2 8.5 + - - -
84B VAL* 3.5 23.5 - - + +
94B ILE* 4.5 8.1 - - + -
95B TYR* 2.6 32.6 + - + +
98B LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 40 (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 VAL* 4.1 22.7 - - + -
23B LEU* 4.1 14.4 - - + -
24B MET* 3.9 31.2 - - - +
27B ARG* 5.4 2.9 - - + -
36B ALA* 2.8 22.8 + - + +
37B LYS 4.0 2.2 - - - +
39B ALA* 1.3 73.9 - - - +
41B GLU* 1.3 61.6 + - - +
43B LEU* 3.1 6.6 + - + +
44B VAL* 2.8 48.9 + - + +
95B TYR* 4.5 1.1 - - + -
98B LEU* 4.1 14.8 - - + -
99B TRP* 3.5 36.6 - - + +
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Residues in contact with GLU 41 (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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17B LEU* 5.7 6.3 - - - +
20B VAL* 3.6 29.5 - - + +
37B LYS* 2.8 53.4 + - - +
38B ARG* 3.3 19.5 + - - +
40B ILE* 1.3 71.9 - - - +
42B SER* 1.3 67.7 + - - +
44B VAL* 4.0 1.0 - - - +
45B LYS* 3.0 27.4 + - - +
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Residues in contact with SER 42 (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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38B ARG* 2.7 44.6 + - - +
39B ALA* 3.3 9.9 - - - -
41B GLU* 1.3 75.5 - - - +
43B LEU* 1.3 60.3 + - - -
45B LYS* 3.9 5.4 - - - +
46B LYS* 3.4 44.7 + - - +
82B LEU* 4.8 6.1 - - - +
83B GLN 5.6 0.4 + - - -
84B VAL* 5.2 4.8 - - - +
95B TYR* 3.8 6.7 + - - -
1007G T 4.3 6.1 + - - -
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Residues in contact with LEU 43 (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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39B ALA 3.2 5.1 + - - +
40B ILE* 3.1 6.0 + - - +
42B SER* 1.3 77.9 - - - +
44B VAL* 1.3 67.9 + - + +
46B LYS* 3.4 5.1 + - + +
47B LEU* 3.0 39.7 + - + +
57B LEU* 4.0 22.4 - - + -
74B ILE* 3.6 31.0 - - + -
95B TYR* 3.3 45.3 - - + +
99B TRP* 4.3 6.5 - - + -
128B VAL* 4.0 20.9 - - + -
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Residues in contact with VAL 44 (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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16B CYS* 4.2 27.8 - - + -
19B ILE* 4.2 28.7 - - + -
20B VAL* 4.1 12.1 - - + -
23B LEU* 4.5 7.2 - - + -
40B ILE* 2.8 40.7 + - + +
41B GLU 4.0 2.7 - - - +
43B LEU* 1.3 71.2 - - + +
45B LYS* 1.3 66.7 + - - +
47B LEU* 2.9 16.6 + - - +
48B LYS* 2.9 13.5 + - + +
54B LEU* 4.4 17.5 - - + -
57B LEU* 5.6 1.3 - - + -
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Residues in contact with LYS 45 (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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16B CYS* 5.1 7.7 - - - -
38B ARG* 5.9 4.9 - - - +
41B GLU 3.0 17.5 + - - +
42B SER* 3.9 4.7 - - - +
44B VAL* 1.3 76.9 - - - +
46B LYS* 1.3 66.5 + - + +
48B LYS* 3.1 23.5 + - - +
49B GLU* 4.1 6.8 + - - +
2011H C 4.0 11.2 + - - -
2012H T 2.7 32.3 + - - +
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Residues in contact with LYS 46 (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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42B SER* 3.4 32.8 + - - +
43B LEU* 3.6 9.2 - - + +
44B VAL 3.3 0.6 - - - -
45B LYS* 1.3 81.6 - - + +
47B LEU* 1.3 62.3 + - + +
48B LYS 3.4 0.3 + - - -
49B GLU* 3.5 21.9 + - - +
50B LYS* 4.4 8.4 + - - +
74B ILE* 4.1 37.6 - - + +
75B GLN 6.1 0.2 - - - +
82B LEU* 3.6 25.3 - - - +
95B TYR* 5.6 0.6 + - - -
1007G T 6.3 0.6 - - - -
1008G A 4.2 9.1 + - - -
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Residues in contact with LEU 47 (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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43B LEU* 3.0 31.4 + - + +
44B VAL 2.9 6.9 + - - +
46B LYS* 1.3 74.7 - - - +
48B LYS* 1.3 56.0 + - - +
49B GLU 2.9 6.3 - - - -
50B LYS* 2.9 34.5 + - - +
51B LYS 3.4 0.9 + - - -
53B GLU* 4.3 15.7 - - + +
54B LEU* 3.6 32.5 - - + +
57B LEU* 3.7 30.5 - - + -
72B VAL* 3.8 24.7 - - + -
73B THR 3.9 21.8 - - - +
74B ILE* 5.0 0.9 - - + -
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Residues in contact with LYS 48 (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 ASN* 4.1 11.5 + - - +
14B ASP 3.1 29.3 + - - -
15B ALA* 5.5 0.2 - - - +
16B CYS* 4.1 27.8 - - - -
19B ILE* 4.8 2.7 - - - -
44B VAL* 2.9 14.7 + - + +
45B LYS* 3.1 13.1 + - - +
47B LEU* 1.3 78.2 - - - +
49B GLU* 1.3 69.3 + - - +
50B LYS 3.2 0.4 + - - -
51B LYS* 3.5 54.7 - - - +
54B LEU* 4.0 16.6 - - + -
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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
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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