Contacts of the helix formed by residues 27 - 39 (chain A) in PDB entry 2LKX
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 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TYR 3.7 2.6 + - - -
26A PRO* 1.3 73.8 - - - +
28A MET* 1.3 73.3 + - - +
29A SER* 2.6 41.1 + - - +
30A THR* 2.9 13.5 + - - +
31A ARG* 2.9 25.9 + - - +
80C C 5.0 0.5 - - - +
81C G 3.7 10.8 + - - -
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Residues in contact with MET 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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27A ASP* 1.3 85.4 + - - +
29A SER* 1.3 61.7 + - - +
31A ARG* 3.1 28.1 - - - +
32A GLU* 2.9 36.0 + - - +
42A GLU* 4.4 9.4 - - + +
80C C 3.4 47.8 - - - +
81C G 3.0 15.6 + - - +
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Residues in contact with SER 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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27A ASP* 2.6 28.9 + - - +
28A MET* 1.3 78.3 - - - +
30A THR* 1.3 61.3 + - - +
32A GLU* 3.8 16.0 - - - +
33A GLU* 3.5 24.1 - - - +
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Residues in contact with THR 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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19A THR* 5.3 4.7 - - + -
23A ASN* 4.6 9.6 + - - +
26A PRO* 4.0 20.6 - - + -
27A ASP* 2.9 13.0 + - - +
29A SER* 1.3 81.0 + - - +
31A ARG* 1.3 58.0 + - - +
32A GLU 3.3 1.8 - - - -
33A GLU* 3.0 28.6 + - + +
34A ILE* 3.1 24.3 + - + +
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Residues in contact with ARG 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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26A PRO* 2.9 51.0 + - + +
27A ASP* 2.9 14.2 + - - +
28A MET* 3.1 17.7 + - - +
30A THR* 1.3 75.4 - - - +
32A GLU* 1.3 59.7 + - - +
34A ILE* 3.6 3.1 + - - +
35A ALA* 3.2 21.0 + - - +
42A GLU* 2.7 44.7 + - + -
45A VAL* 3.6 26.2 - - + +
46A ARG* 3.6 36.9 - - - +
49A PHE* 5.5 2.9 - - - -
81C G 2.8 55.7 + - - -
82C G 4.4 3.3 + - - -
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Residues in contact with GLU 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 MET* 2.9 19.4 + - - +
29A SER* 3.8 16.2 - - - +
31A ARG* 1.3 74.2 - - - +
33A GLU* 1.3 62.5 + - + +
35A ALA* 3.4 9.5 + - - +
36A VAL* 3.0 32.4 + - + +
42A GLU* 4.2 14.0 - - + +
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Residues in contact with GLU 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 SER 3.5 20.3 - - - +
30A THR* 3.0 18.1 + - + +
32A GLU* 1.3 76.0 - - + +
34A ILE* 1.3 60.1 + - + +
36A VAL* 2.9 23.2 + - + +
37A TRP* 3.1 50.1 + - + +
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Residues in contact with ILE 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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15A GLU* 5.5 4.5 - - + +
16A LEU* 3.6 32.3 - - + +
19A THR* 3.9 34.5 - - + +
26A PRO* 4.6 4.3 - - + -
30A THR* 3.1 24.7 + - + +
31A ARG* 3.7 10.3 - - - +
33A GLU* 1.3 73.1 - - + +
35A ALA* 1.3 53.4 + - - +
37A TRP* 3.5 15.8 + - + +
38A THR* 2.8 37.4 + - + +
45A VAL* 3.8 21.3 - - + -
49A PHE* 4.2 11.4 - - + -
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Residues in contact with ALA 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 ARG 3.2 14.6 + - - +
32A GLU* 3.4 11.4 - - - +
33A GLU 3.2 0.2 - - - -
34A ILE* 1.3 74.1 - - - +
36A VAL* 1.3 58.2 + - - +
38A THR* 3.5 5.6 - - - -
39A ASN* 3.0 26.0 + - - -
40A LEU 3.0 33.1 + - - +
41A THR* 3.6 19.3 - - - +
42A GLU 3.9 1.3 - - - +
45A VAL* 3.9 5.8 - - + +
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Residues in contact with VAL 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 GLU* 3.0 22.6 + - + +
33A GLU* 2.9 13.4 + - + +
35A ALA* 1.3 74.3 - - - +
37A TRP* 1.3 88.1 + - + +
38A THR 3.2 1.0 + - - -
39A ASN* 3.5 12.0 + - - +
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Residues in contact with TRP 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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11A GLN* 5.9 3.1 - - - +
15A GLU* 4.7 27.1 - - + +
33A GLU* 3.1 53.8 + - + +
34A ILE* 3.5 15.5 + - + +
35A ALA 3.4 0.4 - - - -
36A VAL* 1.3 96.8 - - + +
38A THR* 1.3 61.5 - - + +
39A ASN 3.8 0.2 - - - -
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Residues in contact with THR 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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11A GLN* 5.1 0.9 - - + +
12A GLN* 3.1 60.0 + - + +
15A GLU* 4.5 18.2 - - + -
16A LEU* 5.2 2.9 - - + -
34A ILE* 2.8 29.1 + - + +
35A ALA* 3.3 6.2 + - - -
37A TRP* 1.3 78.5 - - + +
39A ASN* 1.3 64.6 + - - +
40A LEU* 3.5 20.9 - - + +
45A VAL* 5.1 0.3 - - - +
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Residues in contact with ASN 39 (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 ALA 3.0 7.5 + - - -
36A VAL* 3.5 10.2 + - - +
37A TRP 3.8 0.2 - - - -
38A THR* 1.3 78.7 - - - +
40A LEU* 1.3 65.6 + - - +
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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