Contacts of the helix formed by residues 36 - 50 (chain A) in PDB entry 1YG2
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 5.5 1.4 - - - +
35A ALA* 1.3 73.9 - - - +
37A HIS* 1.3 66.6 + - - +
38A GLN* 3.0 10.9 + - - +
39A GLN* 2.6 41.0 + - - +
40A VAL* 2.9 24.2 + - - +
42A ARG* 4.6 0.2 + - - -
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Residues in contact with HIS 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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22A THR* 3.1 54.5 + - + -
23A LYS* 4.6 0.6 + - - -
25A PHE* 5.7 2.6 - - + +
26A SER* 4.4 17.0 - - - -
35A ALA 4.0 0.2 + - - -
36A SER* 1.3 71.7 - - - +
38A GLN* 1.3 63.8 + - - +
40A VAL* 3.3 9.2 + - - +
41A TYR* 2.9 42.2 + + + -
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 2.9 11.3 - - - +
37A HIS* 1.3 77.9 - - - +
39A GLN* 1.3 65.2 + - - +
41A TYR* 2.9 21.2 + - - +
42A ARG* 2.9 63.5 + - - +
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Residues in contact with GLN 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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3A LEU* 4.0 15.8 - - + +
34A LYS* 4.4 4.2 + - - +
35A ALA* 3.1 12.4 - - + -
36A SER* 2.6 40.7 + - - +
38A GLN* 1.3 78.9 - - - +
40A VAL* 1.3 58.0 + - - +
42A ARG* 3.3 29.7 + - - +
43A GLU* 2.9 30.8 + - - +
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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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3A LEU* 4.7 2.2 - - + -
7A ILE* 4.3 7.9 - - + +
21A ILE* 4.1 22.7 - - + -
22A THR* 4.0 18.8 - - + -
25A PHE* 3.9 39.7 - - + -
35A ALA* 4.1 7.9 - - + -
36A SER 2.9 21.6 + - - +
37A HIS* 3.4 10.8 - - - +
39A GLN* 1.3 76.1 - - - +
41A TYR* 1.3 57.5 + - - +
43A GLU* 3.1 6.7 + - - +
44A LEU* 2.9 34.6 + - + +
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Residues in contact with TYR 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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18A GLY* 3.1 41.6 + - - -
19A TYR* 3.9 4.3 + - - +
22A THR* 3.7 19.6 + - + +
37A HIS* 2.9 34.7 + + + -
38A GLN* 2.9 16.4 + - - +
40A VAL* 1.3 71.2 - - - +
42A ARG* 1.3 64.5 + - + +
44A LEU* 3.3 15.2 + - + +
45A ASN* 3.0 22.7 + - - +
69A TYR* 5.3 6.3 - + - -
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Residues in contact with ARG 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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36A SER* 4.6 0.4 + - - -
38A GLN* 2.9 51.1 + - - +
39A GLN* 3.3 42.6 - - - +
41A TYR* 1.3 77.6 - - + +
43A GLU* 1.3 61.7 + - - +
45A ASN* 3.2 10.1 + - - +
46A LYS* 3.1 26.6 + - - +
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Residues in contact with GLU 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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3A LEU* 3.8 20.8 - - + +
4A PRO* 3.4 32.1 - - + +
7A ILE* 3.7 22.2 - - + -
39A GLN 2.9 16.6 + - - +
40A VAL 3.1 4.5 + - - +
42A ARG* 1.3 73.6 - - - +
44A LEU* 1.3 62.5 + - - +
46A LYS* 3.1 21.0 + - - +
47A MET* 2.8 42.6 + - - +
50A GLN* 4.7 3.5 - - - +
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Residues in contact with LEU 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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7A ILE* 4.1 25.6 - - + -
11A LEU* 4.8 3.8 - - + -
18A GLY* 4.5 4.5 - - - -
21A ILE* 3.8 25.6 - - + -
40A VAL* 2.9 23.5 + - + +
41A TYR* 3.5 24.9 - - + +
43A GLU* 1.3 76.6 - - - +
45A ASN* 1.3 61.9 + - - +
47A MET* 3.4 8.4 + - - +
48A GLY* 3.1 18.9 + - - -
53A VAL* 4.0 15.0 - - + +
69A TYR* 4.0 49.2 - - + +
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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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41A TYR 3.0 12.6 + - - +
42A ARG* 3.2 14.0 + - - +
44A LEU* 1.3 75.0 - - - +
46A LYS* 1.3 70.7 + - - +
48A GLY* 3.0 12.0 + - - -
49A GLU* 3.3 16.1 + - - +
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Residues in contact with LYS 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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42A ARG* 3.1 13.5 + - - +
43A GLU* 3.6 24.7 - - - +
45A ASN* 1.3 84.4 - - - +
47A MET* 1.3 57.3 + - - +
49A GLU* 3.3 10.3 + - - +
50A GLN* 3.0 42.4 + - - +
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Residues in contact with MET 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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4A PRO* 3.8 34.1 - - + +
7A ILE* 4.1 20.0 - - + -
8A LEU* 3.1 42.6 - - + -
43A GLU* 2.8 28.1 + - - +
44A LEU* 3.6 8.1 - - - +
45A ASN 3.1 0.2 - - - -
46A LYS* 1.3 74.7 - - - +
48A GLY* 1.3 60.8 + - - +
50A GLN* 3.3 14.6 + - - +
51A GLY 3.0 5.5 + - - -
52A LEU* 2.9 37.4 + - + +
53A VAL* 3.5 22.1 + - + -
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Residues in contact with GLY 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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44A LEU 3.1 8.4 + - - -
45A ASN 3.0 8.8 + - - -
47A MET* 1.3 75.0 - - - +
49A GLU* 1.3 62.5 + - - +
51A GLY* 3.1 13.3 + - - -
53A VAL* 3.7 21.7 - - - +
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Residues in contact with GLU 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 ASN* 3.3 14.2 + - - +
46A LYS* 3.7 10.8 - - - +
48A GLY* 1.3 75.3 - - - +
50A GLN* 1.3 63.0 + - + +
51A GLY 3.5 0.3 + - - -
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Residues in contact with GLN 50 (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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4A PRO* 5.8 0.5 - - - +
43A GLU* 4.7 3.8 - - - +
46A LYS* 3.0 34.8 + - - +
47A MET* 3.6 14.4 + - - +
48A GLY 3.1 0.4 - - - -
49A GLU* 1.3 81.1 - - + +
51A GLY* 1.3 61.7 + - - +
52A LEU* 3.5 28.9 + - + +
74A ALA* 5.2 2.3 - - - +
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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