Contacts of the helix formed by residues 24 - 38 (chain A) in PDB entry 1K0N
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 CYS 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.6 5.6 - - + -
22A GLY 3.2 8.5 + - - +
23A ASN* 1.3 82.1 - - - +
25A PRO* 1.3 72.2 - - - +
26A PHE* 3.3 12.3 + - - -
27A SER* 3.3 28.8 + - - +
28A GLN* 3.2 20.4 + - - +
65A PRO* 4.7 0.2 - - - -
186A ILE* 4.9 0.9 - - - +
224A PRO* 5.0 2.6 - - - +
1001A GSH 2.0 50.3 - - + -
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Residues in contact with PRO 25 (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 ASN* 4.7 3.4 - - - +
24A CYS* 1.3 86.9 - - - +
26A PHE* 1.3 71.8 + - + +
28A GLN* 3.9 2.1 - - + +
29A ARG* 2.9 29.7 + - - +
111A PHE* 4.1 22.9 - - + -
179A ASN 5.3 0.9 - - - +
182A PRO* 4.0 18.0 - - + +
183A LYS* 3.9 27.8 - - + -
186A ILE* 3.7 26.2 - - + -
1001A GSH 5.4 1.6 - - + -
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Residues in contact with PHE 26 (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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24A CYS* 3.2 9.8 - - - -
25A PRO* 1.3 88.6 - - + +
27A SER* 1.3 66.2 + - - +
29A ARG* 3.3 18.5 + - - +
30A LEU* 3.2 26.5 + - - +
65A PRO* 3.8 11.9 - - + -
77A THR* 3.3 27.7 - - + +
111A PHE* 6.4 1.1 - + - -
183A LYS* 5.6 12.3 - - - -
1001A GSH 3.1 62.6 - - + -
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Residues in contact with SER 27 (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* 4.1 3.9 - - - +
12A VAL* 3.5 39.6 - - - +
13A LYS 3.9 2.8 + - - -
21A ILE* 5.5 4.9 - - - -
22A GLY 5.5 3.4 - - - -
24A CYS* 3.3 27.6 + - - +
26A PHE* 1.3 78.3 - - - +
28A GLN* 1.3 59.4 + - - +
30A LEU* 3.2 4.4 + - - +
31A PHE* 2.9 30.4 + - - +
65A PRO* 4.0 14.5 - - - +
1001A GSH 4.2 0.7 - - - -
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Residues in contact with GLN 28 (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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24A CYS 3.2 11.3 + - - +
25A PRO* 3.9 0.7 - - - +
27A SER* 1.3 79.8 - - - +
29A ARG* 1.3 65.2 + - - +
31A PHE* 3.2 6.9 + - - +
32A MET* 2.9 23.6 + - + +
182A PRO* 3.3 36.4 - - + +
185A HIS* 5.2 1.7 + - - -
186A ILE* 5.8 1.6 - - - +
219A PHE* 3.4 22.6 + - - -
222A THR* 3.0 52.4 + - - +
223A CYS* 3.4 17.2 - - - +
224A PRO* 4.1 9.4 - - + +
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Residues in contact with ARG 29 (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 PRO 2.9 18.8 + - - +
26A PHE* 3.4 17.5 - - - +
28A GLN* 1.3 76.4 - - - +
30A LEU* 1.3 58.2 + - + +
32A MET* 3.2 6.1 + - - +
33A VAL* 3.0 30.3 + - - +
77A THR* 3.8 26.1 - - + +
78A ASN* 2.9 38.7 - - - +
81A GLU* 2.9 40.7 + - - +
178A CYS* 3.2 29.2 - - + +
179A ASN* 3.5 40.3 - - - +
182A PRO* 4.1 0.6 - - - +
183A LYS* 5.6 1.4 - - - +
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Residues in contact with LEU 30 (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* 3.9 24.5 - - + -
26A PHE 3.2 9.0 + - - +
27A SER 3.9 5.2 - - - +
29A ARG* 1.3 74.7 - - + +
31A PHE* 1.3 66.4 + - - +
33A VAL* 3.7 4.9 - - + +
34A LEU* 3.0 30.1 + - + +
65A PRO* 3.8 27.1 - - + -
77A THR* 3.7 27.4 - - + +
80A ILE* 3.8 39.3 - - + -
81A GLU* 4.1 18.6 - - + +
84A LEU* 4.8 5.2 - - + -
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Residues in contact with PHE 31 (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* 3.9 12.7 - - + +
12A VAL* 5.4 2.9 - - + -
21A ILE* 3.7 29.4 - - + -
27A SER* 2.9 13.9 + - - +
28A GLN* 3.2 12.8 + - - +
30A LEU* 1.3 76.9 - - - +
32A MET* 1.3 57.8 + - - +
34A LEU* 3.4 4.0 + - - +
35A TRP* 3.0 39.3 + + - +
41A PHE* 3.7 22.7 - + - -
43A VAL* 3.4 32.1 - - + -
222A THR* 3.6 30.1 - - + -
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Residues in contact with MET 32 (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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28A GLN 2.9 14.1 + - - +
29A ARG 3.5 7.9 - - - +
31A PHE* 1.3 74.8 - - - +
33A VAL* 1.3 65.0 + - - +
35A TRP* 3.4 5.9 + - - +
36A LEU* 2.9 31.4 + - + +
173A LEU* 4.7 14.8 - - + -
177A ASP 4.9 0.4 - - - -
178A CYS* 3.6 28.3 - - + +
181A LEU* 4.2 16.4 - - + -
182A PRO* 4.0 26.0 - - - -
218A GLU* 3.4 22.7 - - + +
219A PHE* 3.9 33.4 - - + +
222A THR* 3.5 9.9 - - - +
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Residues in contact with VAL 33 (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 ARG 3.0 21.3 + - - +
30A LEU* 3.7 10.8 - - + +
31A PHE 3.4 0.2 - - - -
32A MET* 1.3 77.2 - - - +
34A LEU* 1.3 64.0 + - - +
36A LEU 3.3 0.3 + - - -
37A LYS* 3.0 30.2 + - + +
81A GLU* 3.6 29.2 - - + +
84A LEU* 4.2 30.1 - - + -
85A GLU 5.4 0.7 - - - +
96A LEU* 3.7 12.1 - - + +
175A LEU* 3.7 25.4 - - + -
178A CYS* 3.9 12.6 - - + -
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Residues in contact with LEU 34 (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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8A VAL* 4.0 13.2 - - + -
10A LEU* 4.2 16.6 - - + -
30A LEU* 3.0 22.4 + - + +
31A PHE 3.9 0.2 - - - +
33A VAL* 1.3 75.2 - - - +
35A TRP* 1.3 62.4 + - - +
37A LYS* 3.4 4.9 + - - +
38A GLY* 3.3 15.4 + - - -
39A VAL* 3.7 28.9 + - + +
41A PHE* 3.7 41.2 - - + -
67A LEU* 4.1 18.6 - - + -
84A LEU* 3.6 35.4 - - + -
88A LEU* 4.2 3.1 - - + -
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Residues in contact with TRP 35 (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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31A PHE* 3.0 29.7 + + - +
32A MET* 3.7 5.2 - - - +
34A LEU* 1.3 76.8 - - - +
36A LEU* 1.3 57.2 + - - +
38A GLY* 3.0 20.5 + - - -
39A VAL 5.9 0.2 - - - -
41A PHE* 4.0 11.3 - + + -
217A GLU* 3.7 32.5 + - + +
218A GLU* 3.5 32.6 + - + +
221A SER* 3.7 32.5 - - - -
222A THR* 3.7 25.6 - - + -
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Residues in contact with LEU 36 (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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32A MET* 2.9 24.2 + - + +
35A TRP* 1.3 76.0 - - - +
37A LYS* 1.3 62.6 + - - +
38A GLY* 4.5 0.5 - - - -
94A PRO* 3.5 16.8 - - - +
96A LEU* 3.6 25.3 - - + +
173A LEU* 3.8 36.6 - - + +
174A THR 4.9 0.4 - - - +
178A CYS* 3.6 25.8 - - - -
216A ARG* 3.7 13.2 - - - +
218A GLU* 3.6 34.1 - - + +
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Residues in contact with LYS 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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33A VAL* 3.0 28.7 + - + +
34A LEU* 3.6 6.5 - - - +
36A LEU* 1.3 76.7 - - - +
38A GLY* 1.3 58.8 + - - +
39A VAL* 3.3 3.4 - - + +
84A LEU* 4.0 10.8 - - + -
85A GLU* 2.8 38.1 + - - +
88A LEU* 2.6 58.7 + - + +
89A CYS* 4.7 0.6 - - - +
92A ARG 4.9 0.3 - - - +
93A TYR* 3.3 24.5 - - + -
94A PRO* 2.7 42.2 + - - +
95A LYS* 3.9 2.2 - - - +
96A LEU* 3.8 11.9 - - + -
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Residues in contact with GLY 38 (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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34A LEU 3.3 2.3 + - - -
35A TRP* 3.0 16.5 + - - -
36A LEU 3.2 0.9 - - - -
37A LYS* 1.3 78.3 - - - +
39A VAL* 1.3 64.2 + - - +
40A THR* 3.8 1.6 + - - -
93A TYR* 4.4 5.9 - - - -
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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