Contacts of the strand formed by residues 32 - 40 (chain A) in PDB entry 2KE0
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 THR 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY 4.9 1.0 + - - -
31A GLN* 1.3 74.0 + - - +
33A VAL* 1.3 73.7 + - - +
58A ALA* 5.1 4.9 - - + -
59A PHE* 3.7 15.5 - - - +
60A VAL* 3.0 27.3 - - + +
117A VAL 3.6 15.1 - - - -
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Residues in contact with VAL 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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27A ALA* 4.3 9.6 - - + -
31A GLN* 4.0 16.2 - - + +
32A THR* 1.3 82.1 - - - +
34A SER* 1.3 62.2 + - - +
35A VAL* 4.2 17.7 - - + -
57A PHE 4.0 1.4 - - - +
58A ALA* 3.3 1.9 - - - -
59A PHE* 3.0 43.4 + - + +
74A VAL* 4.4 19.5 - - + -
114A LEU* 4.3 6.3 - - + -
116A ASP* 3.3 12.6 - - - +
117A VAL* 3.5 32.1 - - + +
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Residues in contact with SER 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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33A VAL* 1.3 70.1 - - - +
35A VAL* 1.3 64.1 + - - +
56A PRO* 4.7 8.8 - - - +
57A PHE 3.8 4.0 - - - -
58A ALA* 3.2 21.9 - - - +
115A LEU* 2.9 37.8 + - - +
116A ASP* 3.0 34.5 + - - +
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Residues in contact with VAL 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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33A VAL* 4.2 11.0 - - + -
34A SER* 1.3 78.3 - - - +
36A HIS* 1.3 59.4 + - - +
56A PRO 3.5 0.3 - - - -
57A PHE* 2.7 52.3 + - + +
59A PHE* 4.2 16.8 - - + -
70A TRP* 4.9 8.5 - - + -
74A VAL* 5.4 5.6 - - + -
112A VAL* 4.0 20.6 - - + -
113A GLU 3.4 8.5 - - - +
114A LEU* 3.3 39.0 - - + -
115A LEU* 3.9 5.4 - - - -
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Residues in contact with HIS 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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35A VAL* 1.3 73.4 - - - +
37A TYR* 1.3 60.2 + - - +
38A THR* 5.7 0.4 - - - +
50A SER* 3.2 37.8 - - - -
51A LYS* 3.3 22.1 + - + -
54A ASN* 4.4 5.0 + - - -
55A ASP 3.6 0.9 + - - -
56A PRO* 3.3 34.0 - - + +
111A GLU 2.8 14.0 - - - +
112A VAL* 3.2 2.9 - - - -
113A GLU* 2.9 51.2 + - - +
115A LEU* 3.2 30.2 - - + +
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Residues in contact with TYR 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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35A VAL* 6.0 0.4 - - + -
36A HIS* 1.3 75.6 + - - +
38A THR* 1.3 59.8 + - - +
39A GLY 3.9 0.9 + - - -
48A ASP* 4.8 13.2 - - + -
49A SER* 4.1 0.5 - - - -
50A SER* 2.9 48.8 + - - -
51A LYS* 5.0 0.9 + - - +
55A ASP* 4.5 3.9 + - - -
57A PHE* 3.6 38.8 - + + -
70A TRP* 3.5 38.1 - + + -
110A PHE* 3.6 28.5 - + + -
111A GLU 3.2 4.0 - - - -
112A VAL* 4.6 4.7 - - + +
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Residues in contact with THR 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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36A HIS* 4.6 2.1 + - - +
37A TYR* 1.3 72.4 - - - +
39A GLY* 1.3 63.9 + - - +
40A TRP* 3.8 22.1 - - + -
46A LYS* 3.6 19.3 - - + -
48A ASP 3.8 0.9 - - - -
49A SER* 3.3 24.0 - - - +
51A LYS* 5.1 5.7 - - + +
109A VAL 3.4 0.7 - - - +
110A PHE* 3.2 6.3 - - - -
111A GLU* 2.9 56.5 + - - +
113A GLU* 5.0 4.9 + - - -
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Residues in contact with GLY 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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37A TYR 3.9 0.2 + - - -
38A THR* 1.3 72.7 - - - +
40A TRP* 1.3 73.9 + - - -
46A LYS* 3.1 17.2 - - - +
47A PHE* 3.5 15.9 - - - -
48A ASP 2.7 16.8 + - - -
109A VAL 3.4 0.9 - - - -
110A PHE* 3.2 29.6 - - - -
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Residues in contact with TRP 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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38A THR* 3.8 26.2 - - + -
39A GLY* 1.3 85.4 - - - -
41A LEU* 1.3 66.8 + - - +
44A GLY* 3.5 23.2 + - - -
45A GLN 3.4 2.0 - - - -
46A LYS* 3.4 31.9 - - + +
47A PHE* 3.2 12.9 - - - -
84A ARG* 3.9 28.0 - - - +
108A LEU* 3.8 1.6 - - - -
109A VAL* 2.7 51.5 + - + +
111A GLU* 3.5 41.1 - - + -
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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