Contacts of the helix formed by residues 29 - 44 (chain A) in PDB entry 2ORY
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LYS* 1.3 78.0 - - - +
30A ALA* 1.3 60.1 + - - +
31A GLU* 2.8 31.5 + - - +
32A LEU* 2.9 51.3 + - + +
33A ILE* 3.6 16.0 + - - +
60A VAL* 5.1 1.7 - - - +
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Residues in contact with ALA 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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28A LYS 3.5 7.0 + - - +
29A ASN* 1.3 75.0 - - - +
31A GLU* 1.3 54.4 + - + +
33A ILE* 3.2 3.2 + - - -
34A LEU* 2.8 35.9 + - - +
58A PRO* 3.2 34.3 - - + +
60A VAL* 3.9 22.6 - - + +
142A LYS* 5.8 9.9 - - + +
145A ILE* 4.2 16.2 - - + -
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Residues in contact with GLU 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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28A LYS 5.1 2.6 - - - +
29A ASN* 2.8 29.2 + - - +
30A ALA* 1.3 78.8 - - + +
32A LEU* 1.3 65.7 + - - +
34A LEU* 3.5 4.6 + - - +
35A LYS* 3.1 23.2 + - - +
143A SER 5.0 6.0 - - - +
144A HIS* 5.2 8.6 + - + +
145A ILE* 4.0 21.3 - - + -
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Residues in contact with LEU 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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19A GLY* 4.5 5.8 - - - +
22A HIS* 3.4 44.9 - - + +
29A ASN* 2.9 33.5 - - + +
30A ALA 3.3 0.4 - - - -
31A GLU* 1.3 76.2 - - - +
33A ILE* 1.3 74.7 + - + +
35A LYS* 3.5 18.9 + - - +
36A LYS* 3.2 34.1 + - + +
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Residues in contact with ILE 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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16A SER 5.2 0.2 - - - +
18A TYR* 3.7 30.5 - - + +
19A GLY* 4.8 4.9 - - - +
29A ASN 3.6 10.7 + - - +
30A ALA 3.2 6.8 + - - +
32A LEU* 1.3 85.2 - - + +
34A LEU* 1.3 65.7 + - - +
36A LYS* 2.9 9.1 + - - +
37A MET* 2.8 50.9 + - + +
58A PRO* 3.9 9.9 - - + -
60A VAL* 4.0 27.6 - - + -
72A MET* 4.1 9.4 - - + -
90A ARG* 4.0 16.6 - - - +
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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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30A ALA 2.8 20.7 + - - +
31A GLU* 3.8 6.5 - - - +
32A LEU 3.4 0.2 - - - -
33A ILE* 1.3 72.3 - - - +
35A LYS* 1.3 64.6 + - - +
37A MET* 3.1 6.0 + - - +
38A LYS* 3.1 55.1 + - + +
54A VAL* 4.0 24.7 - - + -
57A GLY 4.3 1.3 - - - +
58A PRO* 3.8 24.2 - - + +
144A HIS 4.6 5.2 - - - +
145A ILE* 4.2 13.9 - - + -
146A PRO* 3.7 24.0 - - + -
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Residues in contact with LYS 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 GLU 3.1 14.2 + - - +
32A LEU* 3.6 18.9 - - - +
33A ILE 3.2 0.2 - - - -
34A LEU* 1.3 80.5 - - - +
36A LYS* 1.3 80.5 + - - +
38A LYS* 3.5 9.2 + - - +
39A GLU* 3.3 21.8 + - + +
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Residues in contact with LYS 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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18A TYR* 3.8 46.2 - - + -
19A GLY 5.8 0.2 - - - +
22A HIS* 5.6 5.6 - - - -
32A LEU* 3.2 28.5 + - + +
33A ILE 2.9 8.8 + - - +
35A LYS* 1.3 95.7 - - - +
37A MET* 1.3 66.2 + - - +
39A GLU* 3.3 22.6 + - - +
40A ALA* 3.0 23.2 + - - +
330A ASP* 4.9 11.3 + - - +
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Residues in contact with MET 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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15A MET* 3.9 37.0 - - + +
18A TYR* 5.2 0.7 - - + -
33A ILE* 2.8 35.8 + - + +
34A LEU* 3.1 5.8 + - - +
36A LYS* 1.3 73.2 - - + +
38A LYS* 1.3 56.3 + - - +
40A ALA* 3.2 2.8 + - - +
41A LEU* 2.8 35.3 + - - +
54A VAL* 4.3 14.4 - - + -
58A PRO* 4.1 16.6 - - - -
72A MET* 3.4 21.3 - - + -
74A TYR* 3.3 52.3 - - + -
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Residues in contact with LYS 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* 3.1 50.9 + - + +
35A LYS* 3.8 8.3 - - - +
37A MET* 1.3 75.4 - - - +
39A GLU* 1.3 64.6 + - - +
41A LEU* 3.5 9.9 + - + +
42A LYS* 3.5 19.9 + - - +
53A GLU* 5.5 7.3 + - - -
54A VAL* 5.1 9.9 - - + -
146A PRO* 5.8 1.9 - - - +
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Residues in contact with GLU 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 LYS* 3.3 11.9 + - + +
36A LYS* 3.3 28.1 + - - +
38A LYS* 1.3 78.3 - - - +
40A ALA* 1.3 62.6 + - - +
42A LYS* 3.1 20.2 + - - +
43A THR* 3.0 38.9 + - + +
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Residues in contact with ALA 40 (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 MET* 3.7 15.7 - - - -
18A TYR* 4.1 7.9 - - + +
36A LYS 3.0 13.9 + - - +
37A MET 3.5 7.2 - - - +
39A GLU* 1.3 73.5 - - - +
41A LEU* 1.3 56.1 + - - +
42A LYS 2.7 15.1 + - - -
43A THR* 3.9 1.3 - - - -
44A TRP* 2.9 64.2 + - + +
47A PHE* 3.5 2.8 - - - -
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Residues in contact with LEU 41 (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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12A PHE* 3.9 17.9 - - + -
15A MET* 4.1 12.1 - - + -
37A MET 2.8 22.1 + - - +
38A LYS* 4.0 8.3 - - + +
39A GLU 3.4 0.2 - - - -
40A ALA* 1.3 72.0 - - - +
42A LYS* 1.3 56.3 + - - +
47A PHE* 3.6 48.3 - - + +
48A GLN* 5.4 0.3 - - - -
50A ASP 5.3 0.7 - - - +
52A TRP* 3.9 46.5 + - + +
53A GLU* 4.7 0.2 - - - -
54A VAL* 3.8 30.1 - - + +
76A ILE* 4.4 4.9 - - + -
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Residues in contact with LYS 42 (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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38A LYS 3.5 9.1 + - - +
39A GLU* 3.1 22.2 + - - +
40A ALA 2.7 2.2 + - - -
41A LEU* 1.3 81.3 - - - +
43A THR* 1.3 73.7 + - + +
48A GLN* 4.2 14.3 + - - +
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Residues in contact with THR 43 (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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39A GLU* 3.0 29.2 + - + +
40A ALA* 2.9 1.2 + - - -
42A LYS* 1.3 99.8 - - - +
44A TRP* 1.3 80.0 + - - +
45A LYS* 3.3 4.0 + - - +
48A GLN* 3.3 16.6 + - - +
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Residues in contact with TRP 44 (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 ALA* 3.4 32.3 - - + -
14A TYR* 4.8 0.2 - - + -
15A MET* 3.8 15.3 - - + -
18A TYR* 3.4 28.1 + + - -
40A ALA* 2.9 31.4 + - + +
43A THR* 1.3 85.6 + - - +
45A LYS* 1.3 67.2 + - - +
46A PRO* 4.2 5.4 - - + -
47A PHE* 3.0 47.6 + + + +
48A GLN* 3.2 10.7 + - - +
325A ASP 4.2 12.1 - - - +
326A ILE* 4.3 8.7 - - + -
327A PRO* 3.4 35.3 - - + +
331A ILE* 3.4 26.0 - - + -
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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