Contacts of the helix formed by residues 29 - 44 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B HIS* 5.7 0.4 - - - +
25B SER 4.0 1.6 + - - +
26B ALA* 3.0 21.9 + - - +
27B LYS 3.4 0.4 - - - -
28B LYS* 1.3 74.6 - - - +
30B ALA* 1.3 60.1 + - - +
31B GLU* 3.0 16.0 - - - +
32B LEU* 2.9 47.5 + - + +
33B ILE* 3.5 20.9 + - - +
142B LYS* 5.1 1.1 - - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS 2.8 10.8 + - - +
29B ASN* 1.3 70.9 - - - +
31B GLU* 1.3 61.4 + - - +
33B ILE* 3.2 12.3 + - - +
34B LEU* 2.9 29.4 + - - +
58B PRO* 3.6 26.8 - - - +
59B ALA* 5.5 1.1 - - - -
60B VAL* 5.2 8.1 - - + +
142B LYS* 4.5 13.1 - - + +
145B ILE* 3.9 20.6 - - + -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 3.0 9.5 - - - +
30B ALA* 1.3 79.3 - - + +
32B LEU* 1.3 63.2 + - - +
34B LEU* 3.4 9.8 + - + +
35B LYS* 2.9 23.6 + - - +
143B SER 4.3 2.6 - - - +
144B HIS* 3.9 31.0 + - + +
145B ILE* 4.3 17.9 - - + +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLY* 5.1 4.0 - - - -
22B HIS* 3.7 34.8 - - + +
29B ASN* 2.9 34.8 - - + +
31B GLU* 1.3 75.5 - - - +
33B ILE* 1.3 70.7 + - + +
35B LYS* 3.2 18.3 + - - +
36B LYS* 3.0 37.3 + - + +
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER 5.2 0.2 - - - +
18B TYR* 3.7 30.7 - - + +
19B GLY* 4.7 7.9 - - - -
22B HIS* 5.9 0.7 - - + -
27B LYS 4.9 5.4 - - - +
29B ASN 3.5 17.2 + - - +
30B ALA* 3.2 8.0 + - - +
32B LEU* 1.3 82.1 - - + +
34B LEU* 1.3 58.0 + - - +
36B LYS* 3.2 8.0 + - - +
37B MET* 2.9 57.3 + - + +
58B PRO* 3.9 9.4 - - + -
60B VAL* 4.0 26.5 - - + -
72B MET* 4.5 6.3 - - + -
90B ARG* 4.4 11.4 - - - +
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 2.9 16.7 + - - +
31B GLU* 3.7 8.7 - - + +
32B LEU 3.3 0.2 - - - -
33B ILE* 1.3 76.5 - - - +
35B LYS* 1.3 63.3 + - - +
37B MET* 2.9 6.6 + - + +
38B LYS* 2.9 54.8 + - + +
54B VAL* 4.1 26.0 - - + -
57B GLY 4.4 0.7 - - - +
58B PRO* 3.7 24.6 - - + +
144B HIS 4.7 8.5 - - - +
145B ILE* 4.8 6.3 - - + -
146B PRO* 3.8 26.2 - - + -
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU 2.9 14.8 + - - +
32B LEU* 3.2 21.5 + - - +
34B LEU* 1.3 77.9 - - - +
36B LYS* 1.3 75.3 + - - +
37B MET 3.2 0.2 + - - -
38B LYS* 3.3 9.4 + - - +
39B GLU* 3.2 44.6 + - + +
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TYR* 3.8 43.1 - - + -
19B GLY 5.8 1.1 - - - +
32B LEU* 3.0 29.7 + - + +
33B ILE 3.5 6.7 - - - +
35B LYS* 1.3 88.8 - - - +
37B MET* 1.3 61.7 + - - +
39B GLU* 3.4 25.1 + - - +
40B ALA* 3.1 22.2 + - - +
330B ASP* 3.3 33.5 + - - -
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Residues in contact with MET 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 3.9 36.4 - - + +
18B TYR* 4.9 1.8 - - + -
33B ILE* 2.9 26.2 + - + +
34B LEU* 2.9 8.0 + - - +
36B LYS* 1.3 75.6 - - - +
38B LYS* 1.3 66.5 + - - +
40B ALA* 3.2 3.6 + - - +
41B LEU* 3.1 27.4 + - - +
54B VAL* 4.5 12.6 - - + -
58B PRO* 4.0 28.3 - - + -
72B MET* 3.4 33.0 - - + -
74B TYR* 3.5 35.7 - - + -
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 2.9 48.9 + - + +
35B LYS* 3.8 9.6 - - - +
37B MET* 1.3 75.5 - - + +
39B GLU* 1.3 63.3 + - + +
41B LEU* 3.3 22.7 + - + +
42B LYS* 3.4 30.0 + - - +
54B VAL* 5.7 2.7 - - + -
146B PRO* 6.2 0.4 - - - -
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 3.2 39.2 + - + +
36B LYS* 3.5 30.7 + - - +
37B MET 3.2 0.2 - - - -
38B LYS* 1.3 77.8 - - + +
40B ALA* 1.3 61.7 + - - +
42B LYS* 3.0 13.4 + - - +
43B THR* 3.0 28.0 + - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 3.7 17.5 - - - -
18B TYR* 4.0 7.4 - - + +
36B LYS 3.1 10.8 + - - +
37B MET 3.2 7.8 + - - +
39B GLU* 1.3 78.6 - - - +
41B LEU* 1.3 60.5 + - - +
43B THR* 4.5 0.9 - - - -
44B TRP* 2.8 71.0 + - + +
47B PHE* 3.6 2.3 - - - -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 4.4 6.1 - - + -
15B MET* 4.2 15.3 - - + -
37B MET 3.1 18.8 + - - +
38B LYS* 3.6 15.7 - - + +
39B GLU 3.2 0.4 - - - -
40B ALA* 1.3 76.0 - - - +
42B LYS* 1.3 61.4 + - + +
47B PHE* 3.9 39.0 - - + +
48B GLN* 4.2 8.8 - - - +
52B TRP* 3.6 46.6 - - + +
53B GLU* 4.3 3.4 - - - -
54B VAL* 4.1 24.2 - - + +
76B ILE* 4.6 1.8 - - + -
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS* 3.4 27.4 - - - +
39B GLU* 3.0 10.9 + - - +
41B LEU* 1.3 81.1 - - + +
43B THR* 1.3 60.6 + - - +
48B GLN* 3.1 23.1 + - - +
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLU* 3.0 16.9 + - - +
40B ALA* 3.1 1.5 + - - -
42B LYS* 1.3 81.2 + - - +
44B TRP* 1.3 81.3 + - + +
45B LYS* 3.0 4.3 + - - +
48B GLN* 3.0 16.1 - - - +
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Residues in contact with TRP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.5 32.8 - - + -
15B MET* 3.8 15.0 - - + -
18B TYR* 3.5 26.6 + + - -
40B ALA* 2.8 40.9 + - + +
43B THR* 1.3 84.7 - - + +
45B LYS* 1.3 67.5 + - - +
46B PRO* 4.0 7.0 - - + -
47B PHE* 2.9 44.4 + + + +
48B GLN* 3.4 8.7 + - - +
325B ASP 4.2 13.2 - - - +
326B ILE* 4.3 11.4 - - + -
327B PRO* 3.4 32.0 - - + +
331B ILE* 3.5 25.1 - - + -
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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