Contacts of the strand formed by residues 42 - 51 (chain T) in PDB entry 4PJO
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 MET 42 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28R PRO* 3.7 4.5 - - - -
78S MET* 6.0 1.3 - - + -
80S LYS* 5.2 2.5 - - + -
11T LEU* 4.7 6.3 - - + -
21T VAL* 3.9 30.7 - - - -
33T LEU* 4.4 3.1 - - + -
35T SER 3.7 4.5 - - - +
36T VAL* 4.3 14.1 - - + -
40T MET* 3.5 23.8 - - + +
41T ASN* 1.3 79.0 - - - +
43T GLN* 1.3 59.7 + - - +
44T LEU* 4.3 12.6 - - + -
62T VAL 3.5 1.7 - - - +
63T LEU* 3.5 1.3 - - - -
64T ILE* 2.7 49.5 + - + +
69T VAL* 3.9 26.0 - - + -
72T ILE* 3.9 27.4 - - + -
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Residues in contact with GLN 43 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R THR 4.3 1.6 - - - +
27R GLY 3.6 0.9 - - - +
28R PRO* 3.4 12.7 - - + +
30R SER* 3.1 24.9 + - - -
31R VAL* 3.9 13.1 - - + +
33T LEU* 3.6 2.3 - - - +
34T VAL* 3.0 46.5 + - + +
35T SER* 2.6 40.1 + - - +
42T MET* 1.3 72.9 - - - +
44T LEU* 1.3 73.0 + - - +
61T GLU* 3.0 32.3 + - + +
62T VAL 3.3 4.9 - - - +
63T LEU* 4.6 0.9 - - - +
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Residues in contact with LEU 44 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T VAL* 4.5 4.3 - - + -
21T VAL* 4.2 16.2 - - + -
29T TYR* 3.8 19.5 - - + +
31T GLY* 3.7 28.5 - - - +
32T TYR 3.6 4.0 - - - +
33T LEU* 4.1 22.2 - - + -
34T VAL* 4.1 1.8 - - - -
42T MET* 4.3 11.7 - - + -
43T GLN* 1.3 84.0 - - - +
45T ALA* 1.3 61.2 + - - +
47T THR* 3.0 27.1 - - + +
61T GLU* 3.5 8.1 - - - +
62T VAL* 2.8 31.1 + - + +
64T ILE* 4.1 13.2 - - + -
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Residues in contact with ALA 45 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T GLY* 3.4 0.9 - - - -
32T TYR* 2.8 36.0 + - + +
34T VAL* 3.6 19.1 - - + -
44T LEU* 1.3 76.7 - - - +
46T ASN* 1.3 76.6 + - + +
47T THR* 3.1 2.6 + - - -
60T GLY 4.1 2.5 - - - -
61T GLU* 4.5 9.2 - - + +
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Residues in contact with ASN 46 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T LYS 3.6 5.7 - - - +
31T GLY* 4.0 2.9 - - - -
32T TYR* 4.0 23.7 - - + -
45T ALA* 1.3 78.0 - - - +
47T THR* 1.3 65.8 + - - +
48T GLU* 3.7 4.0 + - - +
58T HIS* 3.5 31.3 + - - +
60T GLY* 3.7 7.6 + - - -
56c GLU* 3.5 36.7 + - - +
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Residues in contact with THR 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T TYR* 3.9 22.4 - - + -
30T LYS 3.1 11.7 - - - +
44T LEU* 3.0 45.9 + - + +
45T ALA 3.9 0.7 - - - -
46T ASN* 1.3 76.4 - - - +
48T GLU* 1.3 63.2 + - - +
58T HIS* 3.9 3.6 - - - -
59T LEU* 2.9 25.2 + - + -
60T GLY 2.7 25.5 + - - -
62T VAL* 3.8 19.7 - - + +
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Residues in contact with GLU 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T GLU 3.8 0.2 - - - +
29T TYR* 3.4 7.0 - - - -
30T LYS* 2.8 44.4 + - + +
46T ASN 4.7 3.4 - - - +
47T THR* 1.3 77.1 - - - +
49T GLU* 1.3 59.9 + - - +
50T TYR* 3.0 35.2 + - + -
55T LEU* 3.4 22.4 - - + +
57T GLY 3.5 9.6 - - - +
58T HIS* 3.7 27.9 - - + +
59T LEU* 4.3 0.9 - - - +
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Residues in contact with GLU 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N GLY* 3.2 14.8 - - - -
41N ILE* 3.2 19.9 + - - +
42N ALA* 3.1 29.6 + - + +
43N PRO* 4.6 0.3 - - - +
27T MET* 5.1 2.0 - - + -
28T GLU 3.6 4.5 - - - +
29T TYR* 2.6 38.1 + - + -
48T GLU* 1.3 71.5 - - - +
50T TYR* 1.3 62.7 + - - +
51T ILE* 4.2 6.8 - - + +
55T LEU* 3.8 1.0 - - - +
56T SER* 2.7 45.0 + - - -
57T GLY 2.9 15.1 + - - +
59T LEU* 3.6 15.8 - - + +
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Residues in contact with TYR 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T MET* 3.7 16.6 - - + -
27T MET* 3.6 3.1 - - - +
28T GLU* 2.8 60.4 + - + +
30T LYS* 3.2 32.2 + - + -
48T GLU* 3.0 42.0 + - + -
49T GLU* 1.3 77.6 - - - +
51T ILE* 1.3 61.6 + - - +
52T ASP 4.0 0.2 + - - -
53T GLY 3.5 15.7 - - - +
54T ALA* 3.8 5.4 - - - +
55T LEU* 3.3 39.8 - - + +
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Residues in contact with ILE 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N TYR 6.0 0.2 - - - +
39N CYS* 4.6 8.1 - - + -
40N GLY* 3.6 31.4 - - - +
27T MET* 4.2 21.1 - - + +
49T GLU* 4.2 3.6 - - + +
50T TYR* 1.3 70.9 - - - +
52T ASP* 1.3 86.7 + - + +
53T GLY 3.1 2.4 + - - -
54T ALA* 2.9 20.7 + - - +
56T SER* 4.0 25.9 - - - +
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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