Contacts of the helix formed by residues 55 - 70 (chain B) in PDB entry 1KA8
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 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.3 4.3 - - - -
53B VAL 3.5 2.7 + - - -
54B LEU* 1.3 75.9 - - - +
56B LEU* 1.3 56.2 + - - +
57B LYS* 3.4 9.7 + - - +
58B MET* 3.0 30.9 + - - +
59B PHE* 2.7 31.9 + - - +
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Residues in contact with LEU 56 (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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23B MET* 4.0 21.8 - - + -
24B GLY 3.7 17.0 - - - +
25B ASN* 3.6 27.6 - - + -
26B ALA* 5.3 2.7 - - + +
38B TYR* 3.3 35.0 + - + -
55B SER* 1.3 73.1 - - - +
57B LYS* 1.3 56.7 + - - +
59B PHE* 3.5 0.5 - - - +
60B GLY* 2.7 35.2 + - - +
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Residues in contact with LYS 57 (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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55B SER* 3.2 7.4 + - - +
56B LEU* 1.3 83.3 - - - +
58B MET* 1.3 68.1 + - + +
60B GLY* 3.4 2.2 + - - -
61B LEU* 3.2 41.2 + - + +
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Residues in contact with MET 58 (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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64A PRO* 3.7 13.2 - - + +
65A VAL* 3.0 57.4 - - + +
68A LYS* 4.3 20.2 - - + -
54B LEU* 4.2 15.9 - - + -
55B SER* 3.0 27.8 + - - +
57B LYS* 1.3 79.2 - - + +
59B PHE* 1.3 66.9 + - - +
61B LEU* 3.2 19.1 + - + +
62B GLY 3.0 18.2 + - - -
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Residues in contact with PHE 59 (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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5B THR* 4.7 10.3 - - + -
8B PHE* 3.9 23.1 - + - -
9B ILE* 4.4 10.1 - - + -
23B MET* 3.8 31.9 - - + -
37B LEU* 3.9 13.5 - - + -
38B TYR* 3.8 28.5 - + + -
41B TYR* 3.7 39.9 - + + -
54B LEU* 4.0 13.5 - - + +
55B SER 2.7 21.3 + - - +
56B LEU 3.5 3.1 - - - +
58B MET* 1.3 72.0 - - - +
60B GLY* 1.3 65.4 + - - +
62B GLY* 3.2 1.7 + - - -
63B LEU* 2.9 40.1 + - + +
66B MET* 5.1 0.6 - - + +
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Residues in contact with GLY 60 (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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23B MET* 4.4 14.5 - - - +
56B LEU* 2.7 22.5 + - - -
57B LYS* 3.7 2.2 - - - -
58B MET 3.2 0.2 - - - -
59B PHE* 1.3 79.3 - - - +
61B LEU* 1.3 55.4 + - - +
63B LEU* 3.4 2.8 + - - +
64B PRO* 3.0 27.2 - - - +
74B TYR* 5.7 1.2 + - - -
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Residues in contact with LEU 61 (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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61A LEU* 4.5 32.4 - - + +
64A PRO* 5.9 3.8 - - + -
65A VAL* 3.7 13.7 - - + -
57B LYS* 3.2 35.4 + - + +
58B MET* 3.6 25.6 - - + +
60B GLY* 1.3 74.9 - - - +
62B GLY* 1.3 62.6 + - - +
64B PRO* 3.2 12.9 - - - +
65B VAL* 3.4 13.4 - - - +
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Residues in contact with GLY 62 (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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62A GLY* 5.5 0.9 - - - -
65A VAL* 3.8 14.5 - - - +
58B MET 3.0 13.0 + - - -
59B PHE 3.7 1.6 - - - -
61B LEU* 1.3 77.5 - - - +
63B LEU* 1.3 66.9 - - - +
65B VAL* 2.8 20.5 + - - +
66B MET* 3.0 33.2 + - - +
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Residues in contact with LEU 63 (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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9B ILE* 3.6 21.3 - - + -
12B LEU* 4.6 2.5 - - + -
23B MET* 3.3 26.2 - - + -
37B LEU* 3.6 10.8 - - + -
59B PHE* 2.9 27.8 + - + +
60B GLY 3.5 7.2 - - - +
62B GLY* 1.3 72.8 - - - +
64B PRO* 1.3 72.6 - - + +
66B MET* 3.2 7.7 + - - +
67B LEU* 2.9 51.0 + - + +
74B TYR* 3.2 31.0 - - + -
87B LEU* 4.3 6.3 - - + -
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Residues in contact with PRO 64 (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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58A MET* 3.2 21.4 - - + +
61A LEU* 4.9 10.1 - - + -
60B GLY 3.0 21.3 - - - +
61B LEU* 3.2 12.6 - - - +
63B LEU* 1.3 87.7 - - + +
65B VAL* 1.3 62.8 + - + +
67B LEU* 3.7 2.5 - - + +
68B LYS* 3.1 18.2 + - - +
72B LEU 5.2 0.3 - - - +
74B TYR* 3.9 39.8 + - + +
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Residues in contact with VAL 65 (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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54A LEU* 3.2 38.6 - - + -
58A MET* 3.4 27.6 - - + +
61A LEU* 4.0 11.7 - - + -
62A GLY* 3.9 26.9 - - - +
66A MET* 5.1 7.2 - - + -
61B LEU 3.4 21.8 - - - +
62B GLY* 2.8 9.9 + - - +
64B PRO* 1.3 69.1 - - - +
66B MET* 1.3 65.6 - - + +
68B LYS* 3.0 6.4 + - - +
69B GLU* 2.9 23.7 + - - +
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Residues in contact with MET 66 (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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3A ASP* 5.5 0.4 - - - +
65A VAL* 5.0 4.7 - - + -
66A MET* 4.8 9.6 - - + -
69A GLU* 5.5 3.8 - - - +
3B ASP* 5.0 4.0 - - - +
5B THR* 3.2 37.7 - - + -
6B PHE* 3.8 33.7 - - + -
9B ILE* 3.9 18.2 - - + -
54B LEU* 5.0 6.3 - - + -
59B PHE* 5.1 2.7 - - + +
62B GLY* 3.0 39.2 + - - +
63B LEU* 3.9 4.5 - - - +
65B VAL* 1.3 76.6 - - - +
67B LEU* 1.3 63.4 + - - +
69B GLU* 3.0 26.3 + - - +
70B TYR* 3.1 21.6 + - - -
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Residues in contact with LEU 67 (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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9B ILE* 3.8 19.9 - - + +
12B LEU* 4.7 6.7 - - + -
63B LEU* 2.9 31.4 + - + +
64B PRO 3.7 4.3 - - - +
66B MET* 1.3 75.1 - - - +
68B LYS* 1.3 60.0 + - - +
70B TYR* 2.8 21.0 + - - +
71B GLY 3.0 0.2 + - - -
72B LEU* 3.0 45.8 + - + +
73B ASN 4.9 0.2 - - - -
74B TYR* 3.2 50.7 - - + +
87B LEU* 3.8 23.6 - - + -
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Residues in contact with LYS 68 (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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54A LEU* 4.4 15.5 - - + -
58A MET* 3.9 25.8 - - + -
64B PRO 3.1 9.7 + - - +
65B VAL 3.0 10.8 + - - +
67B LEU* 1.3 77.9 - - - +
69B GLU* 1.3 55.0 + - - +
71B GLY* 2.7 25.0 + - - -
72B LEU 3.6 14.1 + - - +
73B ASN* 3.7 23.6 + - - +
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Residues in contact with GLU 69 (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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1A ASP* 4.4 11.5 - - - +
3A ASP* 2.6 34.8 - - - +
4A PRO* 4.3 4.8 - - + +
5A THR* 3.3 26.7 + - - -
52A ASN* 5.1 10.8 + - - +
54A LEU* 4.3 17.3 - - + -
66A MET* 3.2 22.0 - - - +
6B PHE* 3.8 12.6 - - + -
65B VAL 2.9 19.1 + - - +
66B MET* 3.0 21.3 + - - +
68B LYS* 1.3 76.4 - - - +
70B TYR* 1.3 59.2 + - - +
71B GLY 3.2 0.7 + - - -
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Residues in contact with TYR 70 (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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1A ASP* 4.9 13.9 - - + -
6B PHE* 2.6 67.3 + + - -
7B ASP* 3.8 4.5 + - - -
9B ILE* 3.3 29.6 - - + -
10B GLY* 3.4 21.6 + - - -
66B MET 3.1 21.4 + - - -
67B LEU 2.8 9.6 + - - +
69B GLU* 1.3 76.9 - - - +
71B GLY* 1.3 61.7 + - - +
72B LEU* 3.7 20.8 + - + +
90B LYS* 6.2 1.3 - - - -
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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