Contacts of the helix formed by residues 38 - 49 (chain A) in PDB entry 6B9H
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 GLY 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU 3.5 8.5 + - - -
36A THR 3.4 4.4 + - - -
37A ASN* 1.3 75.8 + - - +
39A VAL* 1.3 64.3 + - - +
40A VAL 3.4 2.0 - - - -
41A MET* 3.2 6.9 + - - -
42A ALA* 2.9 20.1 + - - +
61A ILE* 4.5 2.5 - - - -
75A ASN* 4.6 0.4 - - - -
76A LEU* 3.9 12.5 - - - +
79A ILE* 2.9 29.4 - - - +
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Residues in contact with VAL 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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27A ALA* 3.8 14.4 - - + -
37A ASN* 2.9 26.0 + - - +
38A GLY* 1.3 75.7 - - - +
40A VAL* 1.3 66.0 + - + +
42A ALA* 3.2 2.4 + - - +
43A GLN* 2.9 46.5 + - + +
58A LEU* 6.2 1.1 - - + -
61A ILE* 4.2 15.5 - - + -
62A LYS 3.5 25.4 - - - +
63A THR* 4.2 22.0 - - + -
64A GLU 5.3 0.4 - - - +
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Residues in contact with VAL 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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20A ILE* 3.7 31.0 - - + -
25A VAL* 4.1 15.5 - - + -
27A ALA* 3.8 20.9 - - + +
28A PRO 3.2 28.5 - - - +
29A CYS* 3.9 11.0 - - + -
34A ASP 3.9 14.8 + - - +
35A LEU* 4.4 12.3 - - + -
37A ASN* 4.5 0.8 + - - -
38A GLY 3.4 0.6 - - - +
39A VAL* 1.3 75.5 - - - +
41A MET* 1.3 65.4 + - + +
43A GLN* 3.2 4.6 + - - +
44A VAL* 2.9 24.1 + - + +
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Residues in contact with MET 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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20A ILE* 5.5 1.8 - - + -
35A LEU* 3.6 25.5 + - + +
38A GLY* 3.2 9.8 + - - +
40A VAL* 1.3 78.2 - - + +
42A ALA* 1.3 58.2 + - - +
44A VAL* 3.3 6.6 + - - +
45A LEU* 3.0 34.5 + - - +
76A LEU* 3.3 34.1 - - + -
79A ILE* 4.3 8.7 - - + -
115A LEU* 4.1 11.0 - - + -
118A MET* 3.9 26.7 - - + +
119A LEU* 3.7 23.6 - - + -
122A ILE* 3.4 32.8 - - + +
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Residues in contact with ALA 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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38A GLY 2.9 16.5 + - - +
39A VAL 3.6 3.4 - - - +
41A MET* 1.3 75.4 - - - +
43A GLN* 1.3 63.4 + - - +
45A LEU* 3.3 4.0 + - - +
46A GLN* 3.0 21.1 + - - +
57A TRP* 3.7 22.9 - - + -
58A LEU* 3.5 23.2 - - + +
61A ILE* 3.8 23.6 - - + -
79A ILE* 4.3 4.0 - - + +
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Residues in contact with GLN 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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25A VAL* 3.3 18.2 - - + +
26A ASP* 3.2 22.2 + - - +
27A ALA* 3.0 33.0 + - - +
39A VAL* 2.9 37.0 + - + +
40A VAL 3.6 4.0 - - - +
42A ALA* 1.3 77.9 - - - +
44A VAL* 1.3 61.7 + - - +
46A GLN* 3.4 10.2 + - - +
47A LYS* 3.1 25.7 + - - +
58A LEU* 4.5 16.6 - - + -
63A THR* 5.8 2.4 - - - +
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Residues in contact with VAL 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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20A ILE* 4.0 30.1 - - + +
23A PHE* 3.7 39.3 - - + -
25A VAL* 3.8 18.6 - - + -
40A VAL* 2.9 21.8 + - + +
41A MET* 3.6 5.4 - - - +
43A GLN* 1.3 75.7 - - - +
45A LEU* 1.3 57.7 + - - +
47A LYS* 3.0 7.6 + - - +
48A ILE* 2.9 28.0 + - + +
122A ILE* 3.8 23.8 - - + -
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Residues in contact with LEU 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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41A MET 3.0 21.2 + - - +
42A ALA 3.6 4.9 - - - +
44A VAL* 1.3 74.1 - - - +
46A GLN* 1.3 57.4 + - - +
48A ILE* 3.2 6.3 + - + +
49A ASP 3.0 25.5 + - - -
53A PHE* 3.4 46.0 - - + -
57A TRP* 4.0 13.9 - - + -
79A ILE* 3.9 26.5 - - + -
83A ILE* 3.9 15.0 - - + -
122A ILE* 4.2 24.0 - - + -
125A CYS* 4.1 23.3 - - + -
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Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ALA 3.0 13.3 + - - +
43A GLN* 3.5 11.0 - - - +
44A VAL 3.3 0.2 - - - -
45A LEU* 1.3 75.2 - - - +
47A LYS* 1.3 64.3 + - + +
50A PRO* 3.1 34.9 - - + +
53A PHE* 3.2 28.7 + - + +
54A ASP* 4.4 0.8 - - - +
55A GLU* 2.8 38.0 + - - +
58A LEU* 2.7 30.7 - - + +
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Residues in contact with LYS 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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23A PHE* 2.8 37.4 + - + +
24A ASN* 2.8 37.4 + - - -
25A VAL* 3.6 19.6 - - + +
26A ASP* 5.9 0.4 + - - -
43A GLN* 3.1 10.3 + - - +
44A VAL 3.0 8.3 + - - +
46A GLN* 1.3 79.2 - - + +
48A ILE* 1.3 62.7 + - - +
50A PRO* 3.8 7.9 - - - +
131A GLN* 6.1 0.3 - - - +
135A TYR* 3.3 10.4 + - - +
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Residues in contact with ILE 48 (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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19A TRP* 4.5 0.2 - - + -
23A PHE* 3.8 17.3 - - + -
44A VAL* 2.9 25.0 + - + +
45A LEU* 3.2 14.6 + - + +
47A LYS* 1.3 78.0 - - - +
49A ASP* 1.3 64.2 + - + +
50A PRO* 4.1 1.7 - - - +
53A PHE* 5.6 0.7 - - + -
86A TYR* 4.7 1.8 - - + +
122A ILE* 3.8 39.9 - - + +
125A CYS* 4.0 12.8 - - + +
126A ALA* 3.9 21.5 - - + +
129A CYS* 3.9 34.6 - - + +
131A GLN* 4.7 7.6 - - - +
135A TYR* 3.4 11.2 + - - +
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Residues in contact with ASP 49 (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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45A LEU 3.0 6.8 + - - -
46A GLN 3.5 2.2 - - - -
48A ILE* 1.3 81.2 - - + +
50A PRO* 1.3 62.1 - - - +
51A ALA* 3.1 22.0 + - - +
52A TYR* 3.3 13.8 + - - +
53A PHE* 2.9 34.0 + - + +
86A TYR* 2.8 43.2 + - + +
90A ILE* 4.7 4.9 - - - +
129A CYS* 5.1 1.7 - - + +
130A GLU* 5.8 1.4 + - - +
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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