Contacts of the helix formed by residues 25 - 38 (chain A) in PDB entry 1OKC
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 VAL 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER 3.1 14.7 + - - +
22A LYS* 3.8 12.3 - - + +
23A THR 3.3 0.2 - - - -
24A ALA* 1.3 79.4 - - + +
26A ALA* 1.3 63.9 + - - +
27A PRO* 3.2 3.6 - - - -
28A ILE* 2.9 32.8 - - + +
29A GLU* 2.9 8.9 + - + +
279A ARG* 3.8 26.2 - - + +
282A GLY* 3.4 13.2 - - - +
283A GLY* 3.3 33.4 - - - +
286A VAL* 4.7 1.8 - - + -
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Residues in contact with ALA 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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22A LYS 3.0 13.3 + - - +
23A THR 3.4 14.6 - - - +
25A VAL* 1.3 77.6 - - - +
27A PRO* 1.3 61.0 - - + +
29A GLU* 3.1 9.1 + - - +
30A ARG* 2.8 31.2 + - - +
69A PHE 3.6 5.7 - - - +
70A TRP* 3.5 12.8 - - + -
73A ASN* 3.5 22.0 - - + +
137A ARG* 4.0 10.6 + - - +
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Residues in contact with PRO 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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23A THR 3.8 3.8 - - - +
24A ALA 3.5 13.7 - - - +
25A VAL 3.3 4.9 - - - -
26A ALA* 1.3 94.1 - - + +
28A ILE* 1.3 60.0 + - - +
30A ARG* 3.2 4.7 + - - +
31A VAL* 3.2 26.5 + - - +
69A PHE* 3.6 37.7 - - + +
70A TRP* 3.6 29.2 - - + +
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Residues in contact with ILE 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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25A VAL* 2.9 33.0 - - + +
27A PRO* 1.3 76.3 - - - +
29A GLU* 1.3 64.6 + - - +
31A VAL* 3.3 13.0 + - + -
32A LYS* 3.0 22.0 + - - +
53A ILE* 4.5 15.3 - - + -
57A VAL* 5.6 2.5 - - + -
275A SER* 3.7 35.2 - - - +
278A LEU* 4.3 13.9 - - + -
279A ARG* 3.7 25.8 - - - +
801A CDL 6.4 0.2 - - + -
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Residues in contact with GLU 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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22A LYS 5.1 0.7 - - - +
25A VAL* 2.9 18.7 + - + +
26A ALA* 3.5 5.9 - - - +
28A ILE* 1.3 78.2 - - - +
30A ARG* 1.3 58.7 + - - +
32A LYS* 3.3 11.7 + - + +
33A LEU* 2.9 37.6 + - + +
76A ASN* 3.1 16.7 + - - +
137A ARG* 2.8 41.7 + - - +
235A ARG* 5.4 5.9 + - - -
279A ARG* 3.8 25.3 + - + +
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Residues in contact with ARG 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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26A ALA 2.8 13.3 + - - +
27A PRO* 3.2 8.7 + - + +
29A GLU* 1.3 75.4 - - - +
31A VAL* 1.3 59.0 + - + +
33A LEU* 3.3 6.8 + - - -
34A LEU* 2.7 51.9 + - + +
60A ILE* 4.4 13.0 - - - +
64A GLN* 2.8 30.2 + - - +
68A SER* 2.8 47.0 + - - -
69A PHE* 3.8 15.3 - - + +
71A ARG* 3.8 13.8 - - - +
137A ARG* 4.5 4.7 - - - +
141A ALA* 2.9 29.2 + - + +
143A ASP 2.7 31.5 + - - -
144A VAL* 4.1 4.9 - - - +
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Residues in contact with VAL 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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27A PRO 3.2 16.7 + - - +
28A ILE* 3.6 12.8 - - + +
29A GLU 3.3 0.2 - - - -
30A ARG* 1.3 75.2 - - + +
32A LYS* 1.3 64.7 + - - +
34A LEU* 3.2 2.3 + - - +
35A LEU* 3.0 32.7 + - + +
53A ILE* 3.9 22.7 - - + -
56A CYS* 3.8 37.0 - - + -
57A VAL* 3.8 24.7 - - + +
60A ILE* 6.0 0.7 - - + -
69A PHE* 4.8 8.3 - - + -
275A SER* 4.0 6.5 - - - +
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Residues in contact with LYS 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 ILE 3.0 14.3 + - - +
29A GLU* 3.4 16.7 + - + +
31A VAL* 1.3 77.4 - - - +
33A LEU* 1.3 76.2 + - + +
35A LEU* 3.9 2.1 - - - +
36A GLN* 2.8 58.8 + - - +
228A TYR* 3.5 14.1 - - - +
231A ASP* 2.8 18.5 + - - -
235A ARG* 3.8 9.3 - - - +
272A GLY* 3.4 23.4 - - - +
275A SER* 3.6 19.3 - - - -
276A ASN* 3.7 28.9 - - + +
279A ARG* 5.6 0.9 - - + +
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Residues in contact with LEU 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 GLU* 2.9 28.6 + - + +
30A ARG 3.7 4.0 - - - +
32A LYS* 1.3 99.7 - - + +
34A LEU* 1.3 61.3 + - + +
36A GLN* 3.3 10.9 + - - +
37A VAL* 2.9 39.0 + - + +
137A ARG* 3.6 30.7 - - - +
138A THR* 4.3 11.0 - - + +
141A ALA* 3.6 30.7 - - + -
142A ALA 5.6 0.4 - - - +
235A ARG* 4.0 24.2 - - + +
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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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30A ARG* 2.7 52.6 + - + +
31A VAL 3.7 2.7 - - - +
33A LEU* 1.3 73.5 - - + +
35A LEU* 1.3 59.3 + - - +
37A VAL* 4.6 2.7 - - + -
38A GLN* 2.8 38.2 + - + +
44A ILE* 4.4 7.0 - - + -
50A TYR* 3.9 24.9 - - + -
56A CYS* 4.3 9.6 - - - -
60A ILE* 5.9 2.7 - - + -
141A ALA 3.0 32.1 - - - +
142A ALA* 4.0 9.9 - - - +
144A VAL* 3.7 29.2 - - + -
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Residues in contact with LEU 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 VAL* 3.0 32.2 + - + +
32A LYS 3.9 2.7 - - - +
34A LEU* 1.3 77.0 - - - +
36A GLN* 1.3 62.4 + - - +
38A GLN* 3.8 30.6 + - - +
39A HIS 5.2 0.3 + - - -
50A TYR* 3.8 19.3 - - + +
51A LYS 4.8 0.4 - - - -
52A GLY* 3.9 28.3 - - - +
53A ILE* 4.1 3.1 - - + +
56A CYS* 5.2 1.3 - - - -
236A ARG* 5.1 0.2 + - - -
271A LYS* 3.6 21.5 - - + +
272A GLY* 4.1 10.5 - - - +
275A SER* 3.8 17.9 - - - +
801A CDL 3.8 20.9 - - - +
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Residues in contact with GLN 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 LYS* 2.8 43.3 + - - +
33A LEU* 3.6 9.8 - - - +
34A LEU 3.2 0.2 - - - -
35A LEU* 1.3 78.9 - - - +
37A VAL* 1.3 62.7 + - + +
228A TYR* 3.2 14.3 + - - +
231A ASP* 2.8 17.5 - - - +
232A THR* 2.9 38.7 + - + +
235A ARG* 3.3 23.5 - - - +
236A ARG* 2.8 27.4 + - - -
271A LYS* 3.4 18.8 + - - +
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Residues in contact with VAL 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 LEU* 2.9 22.9 + - + +
34A LEU* 4.4 2.5 - - + +
36A GLN* 1.3 84.9 - - + +
38A GLN* 1.3 62.6 + - - +
39A HIS 3.0 3.4 - - - -
40A ALA* 2.8 26.3 + - - +
41A SER 3.6 2.9 + - - -
138A THR* 4.7 7.9 - - + -
142A ALA* 3.8 28.3 - - + -
235A ARG* 3.4 40.6 - - + +
236A ARG* 3.7 7.4 - - - +
239A MET* 3.8 19.0 - - + +
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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
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34A LEU* 2.8 24.3 + - - +
35A LEU* 3.8 26.1 + - - +
36A GLN 3.8 0.4 - - - -
37A VAL* 1.3 73.3 - - - +
39A HIS* 1.3 64.3 + - + +
40A ALA 3.1 0.2 - - - -
41A SER* 3.1 25.4 + - - +
44A ILE* 3.6 25.2 - - + +
49A GLN* 3.3 37.2 + - + +
50A TYR* 2.7 55.1 + - + +
271A LYS* 6.2 1.0 - - + +
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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