Contacts of the helix formed by residues 41 - 57 (chain A) in PDB entry 2KG9
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 ASP 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLY 3.6 5.2 + - - +
40A TYR* 1.3 75.4 - - - +
42A SER* 1.3 62.2 + - - +
43A LEU* 2.8 32.7 + - - +
44A ALA* 3.2 17.5 + - - +
45A LEU* 2.9 30.4 + - - +
87A PSR 5.1 0.7 + - - -
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Residues in contact with SER 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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41A ASP* 1.3 76.6 + - - +
43A LEU* 1.3 61.1 + - - +
46A MET* 3.1 26.3 + - - +
87A PSR 1.6 94.1 + - - +
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Residues in contact with LEU 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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41A ASP* 2.8 17.4 + - - +
42A SER* 1.3 73.5 + - - +
44A ALA* 1.3 71.0 + - + +
46A MET* 3.0 41.4 - - + +
47A GLU* 3.1 15.6 + - + +
87A PSR 4.5 9.4 - - - +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER* 3.4 8.8 - - - +
39A GLY 4.5 3.4 - - - +
40A TYR* 3.3 29.3 - - + -
41A ASP* 3.2 26.3 + - - +
43A LEU* 1.3 85.6 - - + +
45A LEU* 1.3 61.8 + - - +
47A GLU* 3.2 14.6 + - - +
48A THR* 3.1 15.8 + - - -
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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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35A PHE* 3.6 54.3 - - + -
40A TYR* 3.4 13.4 - - + +
41A ASP 2.9 17.4 + - - +
44A ALA* 1.3 76.2 - - - +
46A MET* 1.3 58.1 + - - +
48A THR* 3.1 8.2 + - - -
49A ALA* 2.9 29.6 + - + +
65A ALA* 3.4 24.7 - - + +
66A GLY* 5.6 0.2 - - - -
68A VAL* 4.3 2.2 - - + +
74A LEU* 4.4 18.8 - - + -
87A PSR 3.6 20.6 - - + +
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Residues in contact with MET 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 SER 3.1 17.9 + - - +
43A LEU* 3.0 44.6 - - + +
45A LEU* 1.3 75.8 - - - +
47A GLU* 1.3 69.0 + - - +
49A ALA* 3.5 7.4 - - - +
50A ALA* 2.7 43.1 + - - +
65A ALA* 5.9 0.4 - - + -
87A PSR 3.4 40.8 - - + +
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Residues in contact with GLU 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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17A SER* 3.4 25.1 - - - +
43A LEU* 3.1 24.2 + - + +
44A ALA* 3.4 8.1 - - - +
46A MET* 1.3 91.8 - - + +
48A THR* 1.3 63.2 + - - +
50A ALA* 3.9 5.5 - - - +
51A ARG* 3.0 48.4 + - + +
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Residues in contact with THR 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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10A LEU* 5.0 1.6 - - + -
13A ALA* 3.5 28.9 - - + +
14A LEU* 3.6 29.4 - - + +
17A SER* 2.6 23.6 + - - -
35A PHE* 6.2 0.7 - - + -
40A TYR* 3.2 11.6 - - - -
44A ALA 3.1 10.3 + - - -
45A LEU* 3.2 10.8 + - + -
47A GLU* 1.3 76.1 - - - +
49A ALA* 1.3 62.7 + - - +
51A ARG* 3.2 7.2 + - - +
52A LEU* 3.1 28.5 + - + +
74A LEU* 5.3 5.4 - - + -
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Residues in contact with ALA 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* 2.9 21.5 + - + +
46A MET* 3.5 12.3 - - - +
48A THR* 1.3 77.0 - - - +
50A ALA* 1.3 52.5 + - - +
52A LEU* 3.0 8.5 + - - +
53A GLU* 2.7 43.8 + - - +
60A ILE* 4.0 24.2 - - + +
65A ALA* 5.4 6.1 - - + -
74A LEU* 5.3 5.1 - - + +
78A ILE* 5.0 3.8 - - - -
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Residues in contact with ALA 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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46A MET* 2.7 27.8 + - - +
47A GLU* 3.9 9.9 - - - +
49A ALA* 1.3 72.3 - - - +
51A ARG* 1.3 62.4 + - - +
53A GLU* 3.3 16.3 + - - +
54A SER* 2.7 33.9 + - - +
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Residues in contact with ARG 51 (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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13A ALA* 5.1 0.9 - - + +
16A GLU* 2.7 51.0 + - + +
47A GLU* 3.0 39.4 + - + +
48A THR* 3.3 10.1 - - - +
50A ALA* 1.3 79.1 - - - +
52A LEU* 1.3 65.8 + - + +
54A SER* 4.5 0.5 - - - -
55A ARG* 3.4 48.7 + - - +
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Residues in contact with LEU 52 (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 LEU* 3.7 14.1 - - + -
9A ASP* 4.2 8.7 - - - +
10A LEU* 3.8 15.5 - - + -
13A ALA* 3.5 34.5 - - + -
48A THR* 3.1 10.7 + - + +
49A ALA 3.0 6.5 + - - +
51A ARG* 1.3 75.5 - - + +
53A GLU* 1.3 65.1 - - - +
55A ARG* 3.3 14.4 + - - +
56A TYR* 3.0 56.0 + - + +
58A VAL* 5.0 1.6 - - - -
74A LEU* 4.9 0.2 - - + -
78A ILE* 3.5 31.4 - - + -
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Residues in contact with GLU 53 (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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49A ALA* 2.7 33.9 + - - +
50A ALA* 3.3 19.5 - - - +
52A LEU* 1.3 71.3 - - - +
54A SER* 1.3 61.7 + - - +
57A GLY* 2.8 28.1 + - - -
58A VAL* 2.9 34.8 + - + +
59A SER* 3.8 5.2 + - - -
60A ILE* 2.7 57.2 + - + +
78A ILE* 5.3 0.2 - - - +
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Residues in contact with SER 54 (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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50A ALA* 2.7 22.5 + - - +
51A ARG* 4.5 1.6 - - - -
53A GLU* 1.3 79.7 + - - +
55A ARG* 1.3 64.9 + - - +
57A GLY* 3.7 6.5 + - - -
58A VAL 4.9 1.1 - - - -
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Residues in contact with ARG 55 (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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9A ASP* 4.1 7.3 + - - -
12A ARG* 5.6 8.7 - - - +
13A ALA* 5.9 1.0 - - - +
16A GLU* 4.6 11.3 + - - +
51A ARG* 3.4 51.9 + - - +
52A LEU* 3.3 12.8 + - - +
53A GLU 3.3 0.4 - - - -
54A SER* 1.3 81.6 - - - +
56A TYR* 1.3 101.8 + - + +
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Residues in contact with TYR 56 (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 THR* 5.9 3.6 - - - -
5A LEU* 3.5 19.5 - - + +
9A ASP* 2.6 29.8 + - - -
52A LEU* 3.0 52.9 + - + +
53A GLU 4.5 0.4 - - - +
55A ARG* 1.3 109.6 + - + +
57A GLY* 1.3 63.6 + - - +
58A VAL* 5.1 2.0 - - + -
78A ILE* 5.4 1.1 - - + -
82A LEU* 3.6 27.8 - - + -
85A ALA* 4.1 10.7 - - - +
86A ALA* 4.1 18.3 + - - +
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Residues in contact with GLY 57 (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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53A GLU 2.8 9.1 + - - -
54A SER* 3.7 5.6 + - - -
55A ARG 3.4 3.2 + - - -
56A TYR* 1.3 81.0 - - - +
58A VAL* 1.3 63.8 + - - +
85A ALA* 4.3 6.6 - - - +
86A ALA* 5.1 2.7 + - - +
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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