Contacts of the helix formed by residues 28 - 41 (chain B) in PDB entry 5OC9
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 LYS 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ASP 3.7 3.3 + - - +
27B VAL* 1.4 76.2 - - - +
29B GLU* 1.4 63.4 + - - +
30B GLU* 4.2 12.9 + - + +
31B THR* 3.2 17.0 + - - +
32B LYS* 3.2 19.1 + - - +
145B GLY* 2.8 39.7 + - - +
146B TYR* 3.3 20.4 + - + +
147B PRO* 5.5 1.0 - - - +
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Residues in contact with GLU 29 (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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27B VAL 3.8 2.1 + - - +
28B LYS* 1.4 69.3 - - - +
30B GLU* 1.4 55.9 + - - +
32B LYS* 3.3 34.9 + - - +
33B GLU* 2.9 52.6 + - + +
58B LYS* 5.9 0.7 + - - -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 4.6 12.5 + - + +
29B GLU* 1.4 76.6 - - - +
31B THR* 1.4 60.0 + - - +
33B GLU* 4.0 4.0 + - - +
34B TRP* 3.4 22.9 + - - +
144B PRO* 3.9 14.9 - - + +
145B GLY* 3.4 30.6 + - - -
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 5.7 1.3 - - + -
27B VAL* 3.7 8.3 - - + -
28B LYS* 3.2 15.3 + - - +
30B GLU* 1.4 74.8 - - - +
32B LYS* 1.4 57.5 + - - +
34B TRP* 3.2 10.4 + - + +
35B LEU* 2.9 32.2 + - + +
143B ILE* 3.7 23.1 - - + -
144B PRO 2.7 25.9 + - - +
146B TYR* 3.2 18.5 - - + -
161B LEU* 4.9 2.9 - - + -
166B ILE* 3.9 23.6 - - + -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.9 20.6 - - + -
27B VAL* 3.4 21.6 + - + +
28B LYS 3.2 7.8 + - - +
29B GLU* 3.3 41.3 + - - +
31B THR* 1.4 76.0 - - - +
33B GLU* 1.4 61.5 + - - +
35B LEU* 3.4 7.2 + - - +
36B LYS* 3.0 29.0 + - - +
52B PHE* 4.9 4.7 - - + -
66B ASN* 5.8 0.2 - - - +
68B ASN* 2.8 39.2 + - - +
70B TYR* 3.4 26.4 + - + +
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Residues in contact with GLU 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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29B GLU* 2.9 36.6 + - + +
30B GLU* 4.4 3.8 - - - +
32B LYS* 1.4 75.2 - - - +
34B TRP* 1.3 59.4 + - - +
36B LYS* 3.5 25.9 + - - +
37B ASN* 3.0 28.6 + - - +
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Residues in contact with TRP 34 (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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30B GLU 3.4 18.1 + - - +
31B THR* 3.2 11.5 + - + +
33B GLU* 1.3 76.2 - - - +
35B LEU* 1.4 80.1 + - + +
37B ASN* 3.4 7.4 + - + +
38B ARG* 3.2 35.7 + - + +
140B GLU* 2.8 29.3 + - - +
143B ILE* 3.7 29.6 - - + -
144B PRO* 3.6 35.0 - - + +
151B LEU* 4.2 10.1 - - + -
157B LEU* 3.6 40.4 - - + -
161B LEU* 4.4 18.4 - - + -
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Residues in contact with LEU 35 (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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21B ILE* 4.5 9.2 - - + -
23B LEU* 3.8 35.7 - - + -
31B THR* 2.9 17.3 + - + +
32B LYS 3.7 4.7 - - - +
34B TRP* 1.4 82.8 - - + +
36B LYS* 1.4 64.1 + - - +
38B ARG* 3.5 5.5 + - + +
39B ILE* 3.2 50.0 + - + +
52B PHE* 4.7 7.9 - - + -
135B LEU* 5.2 8.3 - - + -
157B LEU* 6.0 1.8 - - + -
158B LEU* 6.4 1.3 - - + -
161B LEU* 3.7 29.4 - - + -
167B VAL* 4.3 11.7 - - + -
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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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32B LYS 3.0 17.3 + - - +
33B GLU* 3.6 29.6 + - - +
34B TRP 3.3 0.2 - - - -
35B LEU* 1.4 75.9 - - - +
37B ASN* 1.4 55.9 + - - +
39B ILE* 3.4 2.8 + - - +
40B ILE* 3.0 52.9 + - + +
52B PHE* 3.5 44.9 + - + -
54B PRO* 5.2 11.5 - - - +
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Residues in contact with ASN 37 (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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33B GLU 3.0 17.1 + - - +
34B TRP* 3.6 9.4 - - + +
35B LEU 3.3 0.2 - - - -
36B LYS* 1.4 74.3 - - - +
38B ARG* 1.3 60.2 + - + +
40B ILE* 4.9 2.9 - - - -
41B ALA* 2.8 41.9 + - + +
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Residues in contact with ARG 38 (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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34B TRP* 3.2 29.9 + - + +
35B LEU* 3.9 7.9 - - + +
36B LYS 3.5 0.2 - - - -
37B ASN* 1.3 79.0 - - - +
39B ILE* 1.4 61.1 + - - +
40B ILE 3.5 0.2 + - - -
41B ALA* 4.1 3.6 + - - +
46B GLY* 3.7 29.9 + - - -
47B GLY* 3.4 12.8 - - - +
48B ALA 3.3 23.7 + - - +
135B LEU* 3.7 21.1 - - + +
136B ARG 2.8 34.1 + - - +
138B LYS* 4.2 14.4 - - - +
140B GLU* 3.4 29.0 + - - -
157B LEU* 3.6 22.3 - - + +
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Residues in contact with ILE 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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21B ILE* 3.8 17.5 - - + -
35B LEU* 3.2 36.3 + - + +
36B LYS 3.9 3.8 - - - +
37B ASN 3.3 0.2 - - - -
38B ARG* 1.4 70.6 - - - +
40B ILE* 1.4 55.3 + - - +
48B ALA* 2.7 23.7 - - - +
50B LEU* 3.0 36.8 + - + +
52B PHE* 3.7 42.4 - - + -
72B VAL* 4.1 13.2 - - + -
132B LEU* 3.7 15.3 - - + -
135B LEU* 4.0 12.1 - - + -
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Residues in contact with ILE 40 (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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36B LYS* 3.0 40.8 + - + +
37B ASN* 4.2 2.5 - - - +
39B ILE* 1.4 77.7 - - - +
41B ALA* 1.4 70.4 + - - +
42B LYS 3.6 0.5 + - - -
48B ALA 3.6 3.1 - - - +
49B GLN* 3.6 12.8 - - - +
50B LEU 3.4 16.6 - - - +
51B LEU* 4.5 3.6 - - + -
52B PHE* 3.7 37.7 - - + +
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Residues in contact with ALA 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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37B ASN* 2.8 24.8 + - + +
38B ARG* 4.6 2.5 - - - +
39B ILE 3.9 0.2 - - - -
40B ILE* 1.4 73.5 - - - +
42B LYS* 1.3 62.1 + - - +
45B ASP* 5.0 10.1 - - + +
46B GLY 4.3 14.6 - - - +
47B GLY 2.9 11.4 - - - +
48B ALA 2.9 20.6 - - - +
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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