Contacts of the helix formed by residues 36 - 47 (chain A) in PDB entry 2QH5
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLN 3.7 2.2 - - - -
28A PHE 3.5 14.8 - - - -
29A LEU 3.4 19.5 - - - -
30A LYS* 3.9 1.8 - - - +
32A PHE* 4.9 0.4 - - - -
35A LYS* 1.3 74.4 - - - +
37A LEU* 1.3 64.9 + - - +
38A PHE 3.7 1.4 + - - -
39A GLU* 3.2 26.7 + - - +
40A LEU* 2.9 28.3 + - - +
67A GLU* 2.6 28.9 + - - -
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Residues in contact with LEU 37 (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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26A LYS* 5.1 4.7 - - + +
27A GLN* 3.7 18.0 + - - +
29A LEU 4.4 2.6 + - - -
32A PHE* 3.7 33.2 - - + -
36A SER* 1.3 71.9 - - - +
38A PHE* 1.3 52.7 + - - +
40A LEU* 3.2 7.9 + - + +
41A SER* 2.7 38.6 + - - -
110A SER 3.3 11.9 - - - +
111A ASP* 3.9 25.6 - - + +
112A HIS 3.5 27.5 - - - +
113A LEU* 4.0 17.7 - - + +
266A ASP 5.9 1.8 - - - +
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Residues in contact with PHE 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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7A LEU* 4.2 9.9 - - + +
9A SER* 3.2 30.1 - - - -
27A GLN* 3.1 24.7 + - + +
28A PHE* 3.9 14.6 - + + -
36A SER* 3.9 3.6 - - - +
37A LEU* 1.3 78.0 - - - +
39A GLU* 1.3 59.9 + - - +
41A SER* 3.7 2.4 - - - -
42A PHE* 2.8 27.0 + - - +
54A ILE* 3.8 32.5 - - + -
64A ALA* 3.5 41.7 - - + -
67A GLU* 4.0 15.5 - - + +
68A ILE* 3.6 18.2 - - + -
110A SER* 3.6 16.0 + - - -
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Residues in contact with GLU 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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30A LYS* 3.3 32.8 + - - -
34A HIS 5.0 0.2 - - - +
35A LYS* 3.5 30.8 - - + +
36A SER* 3.2 34.0 + - - +
38A PHE* 1.3 79.7 - - + +
40A LEU* 1.3 61.3 + - - +
42A PHE* 3.7 6.9 - - - +
43A LYS* 3.0 30.7 + - - +
67A GLU* 3.7 26.7 - - - +
68A ILE* 4.3 6.3 - - + -
71A GLU* 3.6 18.4 - - - +
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Residues in contact with LEU 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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32A PHE* 4.2 25.8 - - + +
35A LYS* 4.0 31.0 - - + +
36A SER 2.9 26.4 + - - +
37A LEU* 3.4 11.7 - - + +
39A GLU* 1.3 77.5 - - - +
41A SER* 1.3 57.4 + - - +
43A LYS* 3.4 11.1 + - + +
44A ARG* 3.0 43.7 + - - +
112A HIS 5.1 1.1 - - - +
113A LEU* 5.2 11.9 - - + -
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Residues in contact with SER 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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5A ASN* 4.7 1.2 - - - +
7A LEU* 4.2 7.6 - - - +
37A LEU 2.7 15.6 + - - -
38A PHE 3.7 4.3 - - - -
40A LEU* 1.3 68.7 - - - +
42A PHE* 1.3 66.1 + - - +
44A ARG* 3.4 27.2 + - - +
45A ASN* 2.9 31.0 + - - +
108A THR* 5.8 0.7 - - - -
109A PRO 3.7 5.3 + - - -
110A SER* 2.8 39.5 + - - -
112A HIS 3.4 3.6 + - - -
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Residues in contact with PHE 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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5A ASN* 4.8 2.2 - - - +
7A LEU* 3.6 26.4 - - + +
38A PHE* 2.8 17.2 + - + +
39A GLU 3.7 3.8 - - - +
41A SER* 1.3 78.8 - - - +
43A LYS* 1.3 61.0 + - - +
45A ASN* 3.9 1.4 - - - +
46A ALA* 3.0 46.6 + - + +
52A THR* 3.8 27.8 - - + -
54A ILE* 4.0 9.2 - - + -
68A ILE* 3.7 38.4 - - + -
71A GLU* 3.5 35.7 - - + -
72A ILE* 4.8 2.2 - - + -
75A LYS* 5.1 4.0 - - + -
77A VAL* 4.0 22.0 - - + -
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Residues in contact with LYS 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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35A LYS* 3.7 23.9 - - - +
39A GLU 3.0 19.1 + - - +
40A LEU* 3.8 11.2 - - + +
42A PHE* 1.3 82.1 - - - +
44A ARG* 1.3 60.5 + - - +
45A ASN 3.4 0.3 + - - -
46A ALA* 3.5 8.1 + - - +
47A SER* 3.0 23.5 + - - +
71A GLU* 3.5 22.4 - - - +
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Residues in contact with ARG 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 LEU* 3.0 20.4 + - - +
41A SER* 3.4 35.9 + - - +
43A LYS* 1.3 79.7 - - - +
45A ASN* 1.3 70.6 + - - +
47A SER* 3.8 5.5 + - - -
48A LEU* 3.6 19.2 - - - +
108A THR* 5.9 1.8 - - - -
109A PRO 5.0 1.4 + - - -
112A HIS* 2.9 33.5 + - - +
113A LEU* 4.3 1.0 - - - +
114A ILE* 3.5 46.5 + - - +
117A LEU* 4.3 27.4 - - + +
120A TYR* 3.5 42.5 + - + -
188A MET* 5.8 0.8 - - - -
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Residues in contact with ASN 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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5A ASN* 3.4 22.2 - - + +
41A SER* 2.9 24.1 + - - +
42A PHE 3.4 1.6 + - - -
43A LYS 3.3 0.4 - - - -
44A ARG* 1.3 85.8 - - - +
46A ALA* 1.3 66.1 + - - +
47A SER 3.2 3.4 - - - -
48A LEU* 3.1 20.5 + - + +
49A VAL* 3.3 17.2 + - + +
106A ILE* 4.1 9.8 - - + +
108A THR* 3.3 29.9 + - - +
120A TYR* 2.4 33.1 + - - -
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Residues in contact with ALA 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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5A ASN* 4.9 0.2 + - - -
42A PHE* 3.0 42.4 + - + +
43A LYS* 3.5 7.5 + - - +
45A ASN* 1.3 76.8 - - - +
47A SER* 1.3 59.8 + - - +
49A VAL* 3.3 28.3 - - - +
52A THR* 4.6 6.5 - - - +
71A GLU 6.0 0.2 - - - +
75A LYS* 4.9 26.2 + - + +
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Residues in contact with SER 47 (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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43A LYS* 3.0 19.2 + - - +
44A ARG* 3.8 5.6 + - - -
46A ALA* 1.3 75.9 - - - +
48A LEU* 1.3 69.8 + - - +
49A VAL 3.3 2.5 + - - +
75A LYS* 5.5 5.4 - - - +
121A GLU* 5.9 0.2 - - - -
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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