Contacts of the helix formed by residues 27 - 41 (chain B) in PDB entry 2OFK
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLU* 3.1 14.7 + - - +
26B THR* 1.3 79.9 + - - +
28B SER* 1.3 67.7 + - - +
29B ARG* 3.1 14.7 + - - +
30B LYS* 3.0 41.1 + - + +
31B LEU* 3.0 23.6 + - - +
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Residues in contact with SER 28 (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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26B THR 3.6 3.2 + - - -
27B ASP* 1.3 75.1 + - - +
29B ARG* 1.3 57.5 + - - +
31B LEU* 3.3 4.3 + - - +
32B PHE* 2.8 29.6 + - - +
102B TRP* 3.6 21.5 - - - -
106B GLU* 4.5 2.8 + - - -
111B SER* 3.7 7.3 + - - -
112B PHE* 3.7 9.7 + - - -
113B ALA* 3.0 34.5 + - - +
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Residues in contact with ARG 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 ASP* 3.1 10.8 + - - +
28B SER* 1.3 79.9 - - - +
30B LYS* 1.3 57.9 + - + +
32B PHE* 3.5 1.7 - - - +
33B GLU* 2.9 28.0 + - - +
61B HIS 4.7 1.0 + - - -
62B GLN* 3.6 22.5 + - - +
63B PHE* 3.4 24.8 + - + +
64B ASP* 3.7 39.3 + - - +
65B PRO* 4.1 7.3 - - - +
67B ARG* 4.9 3.2 - - - +
102B TRP* 3.5 17.0 - - + -
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Residues in contact with LYS 30 (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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25B GLU* 3.4 41.9 + - + +
27B ASP* 3.0 24.3 + - + +
29B ARG* 1.3 74.0 - - + +
31B LEU* 1.3 63.4 + - - +
33B GLU* 3.4 11.9 + - - +
34B MET* 3.1 26.7 + - - +
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Residues in contact with LEU 31 (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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25B GLU* 3.4 31.9 - - + +
26B THR 4.2 0.4 - - - -
27B ASP 3.0 17.9 + - - +
28B SER* 3.6 5.6 - - - +
30B LYS* 1.3 75.8 - - - +
32B PHE* 1.3 58.4 + - - +
34B MET* 3.2 3.4 + - - +
35B ILE* 3.0 25.8 + - - +
112B PHE* 3.8 12.3 - - + -
113B ALA* 3.7 35.0 - - + -
116B VAL* 3.9 9.4 - - + -
117B TRP* 4.0 3.4 - - - +
165B PHE* 3.3 21.7 - - + -
169B CYS* 3.6 28.9 - - + -
171B LEU* 4.4 7.4 - - + -
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Residues in contact with PHE 32 (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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28B SER 2.8 22.0 + - - +
29B ARG 3.5 3.4 - - - +
31B LEU* 1.3 69.4 - - - +
33B GLU* 1.3 67.2 + - - +
35B ILE* 3.3 11.7 + - + +
36B CYS* 3.1 36.3 + - - -
63B PHE* 3.9 36.8 - + + -
65B PRO* 4.8 0.7 - - + -
68B ILE* 4.1 9.6 - - + -
95B ILE 4.2 2.2 - - - -
98B ASN* 3.5 32.3 - - + -
99B ALA* 3.5 28.0 - - + -
102B TRP* 3.3 39.3 - + + -
112B PHE* 3.7 13.6 - + + -
154B PHE* 4.6 4.9 - + - -
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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 ARG* 2.9 18.0 + - - +
30B LYS* 3.6 10.9 - - - +
32B PHE* 1.3 75.9 - - - +
34B MET* 1.3 61.4 + - + +
36B CYS* 3.2 4.2 + - - +
37B LEU* 2.9 36.6 + - + +
53B ARG* 3.6 12.3 + - - -
57B ARG* 2.8 42.3 + - - +
62B GLN 4.7 3.3 - - - +
63B PHE* 3.5 48.5 - - + +
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Residues in contact with MET 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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16B TYR* 5.1 5.6 - - - -
20B GLU* 5.6 0.9 - - - +
25B GLU* 6.3 0.2 - - + -
30B LYS 3.1 17.1 + - - +
31B LEU 3.2 1.7 + - - +
33B GLU* 1.3 80.8 - - + +
35B ILE* 1.3 56.8 + - - +
37B LEU* 4.2 13.7 - - + -
38B GLU* 2.8 54.5 + - + +
46B TRP* 3.5 36.8 - - + -
53B ARG* 4.6 12.8 - - - -
165B PHE* 4.0 2.2 - - + -
168B ALA* 4.4 8.1 - - + -
169B CYS* 3.5 31.9 - - - -
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Residues in contact with ILE 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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31B LEU 3.0 12.0 + - - +
32B PHE* 3.3 18.4 - - + +
34B MET* 1.3 74.4 - - - +
36B CYS* 1.3 68.2 + - - +
38B GLU* 3.4 2.8 + - - +
39B GLY* 3.0 19.2 + - - -
98B ASN* 5.0 4.9 - - - +
112B PHE* 4.0 22.4 - - + -
149B LEU* 4.4 15.5 - - + -
154B PHE* 4.9 8.1 - - + -
156B PHE 4.7 1.7 - - - +
157B VAL* 3.9 26.2 - - + +
161B ILE* 4.5 7.6 - - + +
162B CYS* 4.4 11.9 - - - -
165B PHE* 3.6 40.7 - - + -
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Residues in contact with CYS 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 PHE* 3.1 50.6 + - - +
33B GLU 3.5 7.0 - - - +
35B ILE* 1.3 79.8 - - - +
37B LEU* 1.3 63.8 + - - +
39B GLY* 3.1 3.9 + - - -
40B GLN* 3.0 27.8 + - - +
63B PHE* 3.9 15.5 - - + -
95B ILE* 4.0 24.9 - - + -
98B ASN* 4.0 20.9 - - - -
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Residues in contact with LEU 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* 2.9 38.8 + - + +
34B MET* 3.9 14.4 - - + +
36B CYS* 1.3 72.3 - - - +
38B GLU* 1.3 63.2 + - - +
40B GLN* 3.1 16.1 + - + +
41B GLN* 3.2 10.6 + - - +
46B TRP* 4.0 15.4 - - + -
49B VAL* 3.8 22.0 - - + +
53B ARG* 3.6 35.0 - - + -
56B TYR* 3.8 42.6 - - + -
63B PHE* 4.3 7.6 - - + -
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Residues in contact with GLU 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 MET* 2.8 35.6 + - + +
35B ILE* 3.7 6.7 - - - +
37B LEU* 1.3 77.6 - - - +
39B GLY* 1.3 62.3 + - - +
41B GLN* 3.2 27.4 + - - +
42B ALA 3.7 3.3 + - - -
46B TRP* 4.1 2.5 - - - -
161B ILE* 3.8 27.4 - - + +
164B SER* 3.1 21.4 - - - +
165B PHE* 3.5 22.6 + - + -
168B ALA* 3.3 10.7 - - - +
801B PGE 2.5 38.4 + - - -
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Residues in contact with GLY 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 ILE 3.0 13.0 + - - -
36B CYS 3.1 4.2 + - - -
38B GLU* 1.3 77.3 - - - +
40B GLN* 1.3 65.7 + - - +
42B ALA* 3.1 20.6 + - - +
91B LYS* 3.8 1.6 - - - -
156B PHE* 3.6 40.0 - - - -
161B ILE* 3.8 6.4 - - - +
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Residues in contact with GLN 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 CYS 3.0 14.9 + - - +
37B LEU* 3.1 13.6 + - - +
39B GLY* 1.3 77.8 - - - +
41B GLN* 1.3 53.9 + - - +
42B ALA 3.2 0.2 - - - -
44B LEU* 3.7 8.8 - - - +
49B VAL* 3.9 10.7 - - + +
56B TYR* 3.0 44.8 + - + +
86B ILE* 4.4 6.3 + - - +
91B LYS* 2.8 75.2 + - - +
92B ILE* 4.4 2.6 - - - +
94B ALA* 4.7 4.0 - - - +
95B ILE* 3.4 20.4 - - + +
156B PHE* 5.8 0.2 - - - +
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Residues in contact with GLN 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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81A GLN* 5.5 8.1 - - - +
37B LEU 3.2 8.9 + - - +
38B GLU* 3.2 22.1 + - - +
39B GLY 3.1 1.0 - - - -
40B GLN* 1.3 76.2 - - - +
42B ALA* 1.3 59.5 + - - +
43B GLY 3.1 0.7 + - - -
44B LEU* 2.7 44.8 + - - +
45B SER* 3.5 22.9 - - - +
46B TRP* 3.5 38.2 - - + +
49B VAL* 3.7 11.2 - - + +
164B SER* 5.4 3.6 + - - -
801B PGE 4.4 5.0 - - - +
906B PGE 3.7 12.7 - - - -
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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