Contacts of the strand formed by residues 44 - 56 (chain B) in PDB entry 3O7O
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.9 3.8 - - - -
39B LYS* 3.8 10.6 - - - +
40B PHE* 3.3 9.3 - - - -
41B ASP* 3.0 55.0 + - - +
42B GLY 3.8 0.4 - - - -
43B GLU* 1.3 91.5 - - + +
45B ILE* 1.3 61.0 + - - +
46B THR* 4.2 17.4 + - + +
246B LYS* 4.0 24.0 - - + +
247B PHE 3.4 14.8 - - - +
248B GLU* 3.6 19.5 - - + +
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Residues in contact with ILE 45 (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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13B PHE* 3.8 11.9 - - + -
15B TRP* 3.7 25.1 - - + -
22B MET* 3.6 41.5 - - + -
38B MET* 4.5 3.1 - - + -
39B LYS 3.2 13.2 - - - +
40B PHE* 4.2 7.9 - - + -
44B LYS* 1.3 74.3 - - - +
46B THR* 1.3 65.8 + - - +
69B PHE* 3.9 21.1 - - + -
245B TRP* 3.8 16.9 - - + -
246B LYS* 3.5 2.1 - - - -
247B PHE* 2.8 47.9 + - + +
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Residues in contact with THR 46 (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 ALA 4.4 0.2 - - - -
38B MET* 3.3 6.8 - - - +
39B LYS* 2.8 56.2 + - - +
44B LYS* 4.2 20.2 - - + +
45B ILE* 1.3 77.7 - - - +
47B PHE* 1.3 60.4 + - - +
48B ASP* 4.7 8.5 + - - -
245B TRP* 3.3 12.3 - - - +
246B LYS* 3.7 29.6 - - + -
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Residues in contact with PHE 47 (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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24B LEU* 3.8 27.4 - - + -
26B LEU* 5.1 4.5 - - + -
36B VAL* 4.0 8.5 - - + -
37B ALA 3.3 20.0 - - - -
38B MET* 3.7 16.2 - - + -
46B THR* 1.3 75.8 - - - +
48B ASP* 1.3 74.4 + - - +
49B ALA* 3.7 24.2 - - + -
67B PRO* 3.5 35.9 - - + -
243B PHE* 3.6 22.0 - + - -
244B GLY* 2.9 3.4 - - - -
245B TRP* 2.7 63.0 + + + +
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Residues in contact with ASP 48 (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 SER 4.1 0.7 - - - +
36B VAL* 3.4 2.8 - - - -
37B ALA* 2.9 39.3 + - + +
46B THR* 4.7 8.3 + - - -
47B PHE* 1.3 91.3 + - - +
49B ALA* 1.3 61.7 + - - +
105B HIS* 3.1 31.6 + - - -
243B PHE 3.6 4.9 - - - +
244B GLY* 4.0 0.2 - - - -
245B TRP 4.8 0.9 - - - +
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Residues in contact with ALA 49 (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 SER 3.4 4.9 - - - -
36B VAL* 3.9 10.5 - - + -
47B PHE* 3.7 23.3 - - + -
48B ASP* 1.3 76.4 - - - +
50B ASP* 1.3 61.1 + - - +
51B ILE* 4.6 7.4 - - + -
233B PHE* 6.0 0.2 - - + -
241B ALA 3.8 5.2 - - - +
242B GLN* 3.3 3.5 - - - -
243B PHE* 2.7 53.0 + - + +
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Residues in contact with ASP 50 (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 GLY* 3.3 6.9 - - - -
35B SER* 2.9 33.4 + - - +
49B ALA* 1.3 74.7 - - - +
51B ILE* 1.3 58.8 + - - +
52B GLN* 2.8 26.6 + - - +
241B ALA 3.5 3.1 - - - -
242B GLN* 3.2 29.1 + - + +
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Residues in contact with ILE 51 (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 LEU* 4.7 2.7 - - + -
29B ILE* 3.8 18.6 - - + -
32B TYR* 3.6 21.1 - - + -
33B SER 3.2 14.4 - - - +
35B SER 3.5 23.6 - - - +
36B VAL* 3.7 18.8 - - + -
49B ALA* 4.6 6.1 - - + -
50B ASP* 1.3 73.9 - - - +
52B GLN* 1.3 66.6 + - - +
54B LEU* 3.6 26.4 - - + +
233B PHE* 4.0 16.6 - - + -
240B SER* 3.3 2.4 - - - -
241B ALA* 2.7 51.4 + - + +
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Residues in contact with GLN 52 (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 TYR* 3.3 5.2 - - - +
33B SER* 2.7 41.2 + - - +
34B GLY* 4.1 9.5 + - - -
50B ASP* 2.8 37.2 + - - +
51B ILE* 1.3 85.0 + - - +
53B ASN* 1.4 68.7 + - - +
54B LEU* 3.2 4.7 + - - +
239B LYS 3.4 7.9 - - - +
240B SER* 3.9 19.9 + - - +
242B GLN* 4.6 3.0 - - - +
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Residues in contact with ASN 53 (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 GLU* 3.2 32.1 - - - +
32B TYR 4.8 1.1 - - - -
33B SER* 2.8 28.0 + - - +
52B GLN* 1.4 79.8 - - - +
54B LEU* 1.3 61.2 + - - +
55B SER* 4.8 0.2 - - - -
239B LYS* 3.2 9.1 + - - +
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Residues in contact with LEU 54 (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 ILE* 4.0 13.7 - - + -
31B GLU 3.4 3.1 - - - +
32B TYR* 3.7 20.9 - - + -
51B ILE* 3.6 28.0 - - + +
52B GLN 4.0 5.2 - - - +
53B ASN* 1.3 75.2 - - - +
55B SER* 1.3 66.7 + - - +
64B LEU* 4.0 13.2 - - + -
238B THR* 3.5 29.1 - - + +
239B LYS* 3.4 48.8 + - - +
240B SER* 3.7 4.7 - - - +
241B ALA* 3.8 22.7 - - + +
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Residues in contact with SER 55 (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 ILE* 3.7 5.5 - - - +
30B LYS* 2.9 36.5 + - - -
31B GLU* 3.2 37.3 + - - +
53B ASN 4.8 0.2 - - - -
54B LEU* 1.3 77.4 + - - +
56B PRO* 1.3 71.0 - - - +
64B LEU* 4.5 5.2 - - - +
238B THR 5.5 0.7 - - - -
239B LYS* 5.6 1.6 + - - -
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Residues in contact with PRO 56 (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 ASN* 3.1 22.0 - - - +
30B LYS* 3.7 9.5 - - - +
55B SER* 1.3 90.4 - - - +
57B LYS* 1.3 63.9 + - - +
59B PRO* 4.0 34.8 - - + +
62B TYR 5.4 0.9 - - - +
64B LEU* 3.8 17.7 - - + -
236B PRO* 4.1 31.2 - - + +
238B THR 6.1 0.7 - - - +
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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