Contacts of the helix formed by residues 58 - 71 (chain A) in PDB entry 2KUM
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 ASN 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 5.1 12.1 - - - +
16A LYS 4.2 10.1 + - - -
17A PRO* 5.6 0.5 - - - +
54A ILE* 3.5 25.3 - - + +
55A HIS* 3.0 24.4 - - + +
56A PRO 3.2 5.3 + - - +
57A GLN* 1.3 74.1 - - - +
59A PRO* 1.3 83.4 - - - +
60A SER* 3.2 27.7 + - - -
61A LEU* 3.0 16.5 + - + +
62A SER* 3.3 12.7 + - - -
88A GLY* 4.1 4.6 + - - -
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Residues in contact with PRO 59 (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 PRO* 6.4 1.8 - - + -
57A GLN 4.5 2.5 - - - +
58A ASN* 1.3 93.4 - - - +
60A SER* 1.3 54.0 + - - +
62A SER* 4.3 8.5 - - - +
63A GLN* 2.7 55.0 + - + +
88A GLY* 4.9 5.1 - - - +
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Residues in contact with SER 60 (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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16A LYS 4.3 1.1 - - - -
17A PRO* 3.6 17.8 - - - +
18A LEU* 3.0 34.9 + - - +
23A LEU* 5.0 6.6 - - - +
45A LEU* 5.1 1.2 - - - +
54A ILE* 4.3 5.9 - - - +
58A ASN* 3.1 23.2 + - - -
59A PRO* 1.3 80.8 - - - +
61A LEU* 1.3 56.8 + - - +
63A GLN* 4.0 11.1 - - - +
64A TRP* 3.1 26.5 + - - +
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Residues in contact with LEU 61 (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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29A VAL* 4.5 4.5 - - + -
43A PHE* 3.5 49.4 - - + +
45A LEU* 3.4 35.4 - - + -
54A ILE* 4.0 14.6 - - + +
56A PRO 4.9 5.8 - - - +
58A ASN* 3.0 11.7 + - + +
60A SER* 1.3 77.8 - - - +
62A SER* 1.3 66.3 + - - +
64A TRP* 3.1 13.0 + - + +
65A PHE* 3.1 44.5 + - + -
84A LEU* 5.0 2.2 - - + -
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Residues in contact with SER 62 (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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56A PRO 5.6 0.3 + - - -
58A ASN 3.3 5.0 + - - -
59A PRO* 3.2 10.7 + - - -
61A LEU* 1.3 78.9 - - - +
63A GLN* 1.3 61.6 + - - +
65A PHE* 3.0 30.2 + - - +
66A GLU* 3.5 9.3 + - - +
84A LEU* 4.5 7.8 - - - +
86A LYS* 3.8 31.5 + - - -
88A GLY* 3.3 33.0 + - - -
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Residues in contact with GLN 63 (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 PRO* 5.6 6.1 - - - +
23A LEU* 6.2 0.9 - - + -
59A PRO* 2.7 41.4 + - + +
60A SER* 4.0 9.3 - - - +
62A SER* 1.3 72.7 - - - +
64A TRP* 1.3 56.5 + - - +
66A GLU* 3.1 14.9 + - - +
67A HIS* 2.8 51.6 + - + +
86A LYS* 3.3 23.2 + - - +
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Residues in contact with TRP 64 (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 LEU* 2.8 59.0 - - + +
24A ARG 4.2 0.4 - - - -
26A VAL* 3.3 26.9 + - + +
29A VAL* 3.6 9.6 - - + +
45A LEU* 3.4 34.6 - - + +
60A SER 3.1 20.9 + - - +
61A LEU* 3.1 12.9 + - + +
63A GLN* 1.3 75.3 - - - +
65A PHE* 1.3 55.7 + - - +
67A HIS* 3.4 25.4 - - + -
68A GLN* 2.6 66.3 + - + +
71A LYS* 3.8 8.5 - - - -
72A LEU* 3.2 26.7 - - + -
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Residues in contact with PHE 65 (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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29A VAL* 4.8 9.4 - - + -
43A PHE* 4.2 13.0 - + - -
61A LEU* 3.1 40.4 + - + -
62A SER* 3.0 15.8 + - - +
64A TRP* 1.3 76.7 - - - +
66A GLU* 1.3 61.0 + - + +
68A GLN* 3.4 24.2 - - - +
69A GLU* 3.4 23.2 + - - +
79A LEU* 5.3 1.8 - - + -
81A PHE* 3.7 55.8 - + + -
84A LEU* 3.6 33.0 - - + -
85A ARG* 4.0 16.6 - - - -
86A LYS 4.9 0.4 - - - +
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Residues in contact with GLU 66 (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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62A SER 3.8 6.7 - - - +
63A GLN* 3.1 17.1 + - - +
65A PHE* 1.3 77.5 - - + +
67A HIS* 1.3 70.6 + - + +
69A GLU* 3.2 22.8 + - - +
70A ARG* 3.3 33.4 + - - +
86A LYS* 2.7 55.4 + - + +
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Residues in contact with HIS 67 (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 ASP* 2.6 32.4 + - + +
23A LEU* 4.6 6.4 - - + +
63A GLN* 2.8 48.9 + - + +
64A TRP* 3.4 21.8 - + + -
66A GLU* 1.3 83.7 + - + +
68A GLN* 1.3 56.9 + - - +
70A ARG* 2.9 23.3 + - - +
71A LYS* 2.8 37.1 + - + +
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Residues in contact with GLN 68 (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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29A VAL* 3.2 17.4 - - - +
64A TRP* 2.6 59.0 + - + +
65A PHE* 3.4 19.5 - - - +
67A HIS* 1.3 73.3 - - - +
69A GLU* 1.3 65.2 + - + +
70A ARG 3.3 0.7 + - - -
71A LYS 3.3 16.6 - - - +
72A LEU* 3.3 27.0 - - + +
74A GLY* 5.9 0.2 - - - -
76A LEU* 3.5 33.9 - - + +
77A PRO* 5.7 0.2 - - - +
79A LEU* 4.6 4.9 - - - +
81A PHE* 3.7 25.2 - - + -
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Residues in contact with GLU 69 (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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65A PHE 3.4 11.4 - - - +
66A GLU* 3.2 17.1 + - - +
68A GLN* 1.3 85.7 - - + +
70A ARG* 1.3 61.2 + - + +
71A LYS 4.8 0.7 - - - +
74A GLY* 6.0 1.6 - - - -
76A LEU* 4.3 7.9 - - + -
81A PHE* 5.6 4.9 - - - -
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Residues in contact with ARG 70 (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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66A GLU* 3.3 31.4 + - - +
67A HIS* 2.9 30.9 + - - +
69A GLU* 1.3 83.9 + - - +
71A LYS* 1.3 70.5 + - + +
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Residues in contact with LYS 71 (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 ASP* 2.6 46.1 + - - +
21A LYS* 5.5 0.2 - - - +
24A ARG* 3.4 46.6 - - + +
64A TRP* 3.8 6.1 - - + -
67A HIS* 2.8 28.5 + - + +
68A GLN 3.3 6.5 + - - +
69A GLU 4.8 0.7 - - - -
70A ARG* 1.3 92.9 - - + +
72A LEU* 1.3 76.0 + - + +
73A HIS* 2.9 13.6 + - - +
74A GLY* 3.1 12.1 + - - -
75A THR 4.6 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