Contacts of the helix formed by residues 35 - 53 (chain B) in PDB entry 3QEK
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 THR 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU 3.5 0.6 - - - -
34B SER* 1.3 92.9 + - - +
36B LYS* 1.3 64.6 + - - +
37B LYS* 3.3 11.5 + - - +
38B HIS* 2.7 47.0 + - + +
39B GLU* 3.1 13.2 + - - +
66B THR* 3.7 10.0 - - - +
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Residues in contact with LYS 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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35B THR* 1.3 73.4 - - - +
37B LYS* 1.3 63.2 + - - +
39B GLU* 3.3 26.2 + - - +
40B GLN* 3.0 20.8 + - - +
43B ARG* 4.7 2.8 + - - -
66B THR* 4.0 6.8 + - + +
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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
----------------------------------------------------------
35B THR* 3.1 11.6 + - - +
36B LYS* 1.3 78.6 - - - +
38B HIS* 1.3 65.6 + - + +
40B GLN* 3.0 12.8 + - + +
41B ILE* 3.0 39.9 + - + +
44B GLU* 5.0 9.5 + - - -
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Residues in contact with HIS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.6 9.8 - - + +
34B SER* 4.1 2.0 - - - -
35B THR* 2.7 43.8 + - + +
37B LYS* 1.3 78.2 - - + +
39B GLU* 1.3 58.8 + - - +
41B ILE* 3.1 18.6 + - + +
42B PHE* 2.9 28.6 + - - +
298B GLU* 3.4 54.1 + - + +
299B SER* 4.1 10.4 + - - -
302B ILE* 3.6 12.7 - - + +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.9 12.1 - - + +
35B THR 3.1 10.8 + - - +
36B LYS* 3.3 34.1 + - - +
38B HIS* 1.3 74.8 - - - +
40B GLN* 1.3 62.9 + - - +
42B PHE* 3.1 5.6 + - - +
43B ARG* 3.0 40.1 + - - +
64B SER* 2.7 47.5 + - - +
65B VAL* 3.6 7.5 + - - +
66B THR* 3.6 19.7 - - + +
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Residues in contact with GLN 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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36B LYS 3.0 11.3 + - - +
37B LYS* 3.0 20.6 + - + +
39B GLU* 1.3 76.2 - - - +
41B ILE* 1.3 61.7 + - - +
43B ARG* 3.3 28.6 + - - +
44B GLU* 3.0 39.3 + - + +
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Residues in contact with ILE 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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37B LYS* 3.0 36.8 + - + +
38B HIS* 3.1 21.1 + - + +
40B GLN* 1.3 75.2 - - - +
42B PHE* 1.3 58.0 + - - +
44B GLU* 3.4 15.4 + - - +
45B ALA* 2.9 26.9 + - - +
299B SER* 3.2 42.4 - - - +
302B ILE* 4.1 15.9 - - + -
303B SER* 4.4 8.3 - - - +
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Residues in contact with PHE 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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29B ILE* 3.4 41.5 - - + -
31B ALA* 3.7 17.7 - - + -
33B LEU* 3.7 12.8 - - + -
38B HIS 2.9 12.8 + - - +
39B GLU 3.1 8.3 + - - +
41B ILE* 1.3 75.8 - - - +
43B ARG* 1.3 58.0 + - + +
45B ALA* 3.1 5.0 + - - +
46B VAL* 3.0 38.8 + - + +
62B ALA* 3.8 18.2 - - + -
63B THR 3.8 9.2 - - - -
64B SER* 3.9 18.6 - - - -
91B LEU* 3.8 20.6 - - + -
302B ILE* 3.5 12.1 - - + +
306B VAL* 3.6 27.1 - - + -
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Residues in contact with ARG 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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36B LYS 4.7 2.4 + - - -
39B GLU* 3.0 31.1 + - - +
40B GLN* 3.3 35.6 + - - +
42B PHE* 1.3 77.8 - - + +
44B GLU* 1.3 59.0 + - + +
46B VAL* 3.1 3.5 + - - +
47B ASN* 2.8 38.8 + - - +
62B ALA* 4.0 26.9 - - + -
64B SER* 4.7 6.6 + - - +
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Residues in contact with GLU 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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37B LYS* 5.0 7.6 + - - -
40B GLN* 3.0 28.8 + - - +
41B ILE* 3.7 14.2 - - - +
43B ARG* 1.3 76.3 - - + +
45B ALA* 1.3 57.2 + - - +
47B ASN* 3.2 15.3 + - - +
48B GLN* 2.9 35.1 + - + +
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Residues in contact with ALA 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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41B ILE 2.9 14.0 + - - +
42B PHE* 3.3 11.0 - - - +
44B GLU* 1.3 76.8 - - - +
46B VAL* 1.3 56.0 + - - +
48B GLN* 3.3 7.7 + - - +
49B ALA* 3.0 28.1 + - - +
302B ILE* 4.5 0.9 - - + +
303B SER* 4.3 23.3 - - - +
306B VAL* 3.6 26.4 - - + +
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Residues in contact with VAL 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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29B ILE* 5.0 7.6 - - + -
42B PHE* 3.0 32.4 + - + +
43B ARG 3.1 6.0 + - - +
45B ALA* 1.3 73.4 - - - +
47B ASN* 1.3 68.7 + - - +
49B ALA* 3.3 3.5 + - - +
50B ASN* 3.1 23.2 + - - +
60B LEU* 3.7 40.8 - - + +
61B GLN 4.1 3.4 - - - +
62B ALA* 4.0 26.7 - - + +
306B VAL* 3.9 19.1 - - + -
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Residues in contact with ASN 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 ARG* 2.8 21.8 + - - +
44B GLU* 3.3 17.5 - - - +
46B VAL* 1.3 78.5 - - - +
48B GLN* 1.3 67.0 + - - +
50B ASN* 3.2 20.6 + - - +
51B LYS* 3.4 29.7 + - - +
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Residues in contact with GLN 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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44B GLU* 2.9 22.9 + - + +
45B ALA* 3.7 7.9 - - - +
47B ASN* 1.3 78.1 - - - +
49B ALA* 1.3 62.7 + - - +
51B LYS* 3.0 40.4 + - - +
52B ARG* 3.1 12.4 + - - +
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Residues in contact with ALA 49 (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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45B ALA 3.0 16.2 + - - +
46B VAL 3.3 5.6 + - - +
48B GLN* 1.3 75.7 - - - +
50B ASN* 1.3 63.1 + - - +
52B ARG* 3.1 15.4 + - - +
53B HIS* 3.3 21.1 + - + +
60B LEU* 4.1 9.0 - - + -
306B VAL* 4.2 10.5 - - + +
307B ALA* 5.4 2.5 - - - -
310B ALA* 3.7 29.2 - - + -
314B HIS* 5.4 0.3 - - - -
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Residues in contact with ASN 50 (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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46B VAL* 3.1 19.8 + - - +
47B ASN* 3.5 15.5 + - - +
49B ALA* 1.3 77.4 - - - +
51B LYS* 1.3 58.5 + - + +
53B HIS* 2.9 22.1 - - - +
58B ILE 4.7 2.3 - - - +
59B GLN* 3.8 12.0 - - - +
60B LEU* 2.8 54.4 + - - +
314B HIS* 5.9 1.9 - - - -
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Residues in contact with LYS 51 (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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47B ASN* 3.4 24.0 - - - +
48B GLN* 3.0 35.5 + - - +
50B ASN* 1.3 78.2 - - + +
52B ARG* 1.3 63.3 + - - +
53B HIS 4.2 1.5 - - - +
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Residues in contact with ARG 52 (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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48B GLN 3.1 8.8 + - - +
49B ALA* 3.1 11.3 + - - +
51B LYS* 1.3 82.2 - - - +
53B HIS* 1.3 72.6 + - + +
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Residues in contact with HIS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.3 18.9 + - + +
50B ASN* 2.9 19.5 - - - +
51B LYS 4.2 1.7 - - - -
52B ARG* 1.3 88.4 - - + +
307B ALA 5.2 0.8 + - - -
310B ALA* 4.1 10.8 - - + +
311B GLN* 3.9 37.5 + - + +
314B HIS* 3.1 50.8 + + + +
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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