Contacts of the strand formed by residues 37 - 44 (chain B) in PDB entry 4J1R
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 VAL 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 1.3 79.1 - - - +
38B THR* 1.3 71.9 + - - +
39B THR* 4.1 6.1 + - + +
55B SER* 4.1 8.7 - - - +
56B TYR 3.8 3.8 - - - +
57B THR* 4.1 9.4 - - + +
76B CYS* 3.6 33.2 - - - -
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Residues in contact with THR 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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36B LYS* 4.1 6.8 + - - +
37B VAL* 1.3 74.9 - - - +
39B THR* 1.3 64.3 + - - +
40B VAL* 4.1 13.2 - - + -
55B SER* 3.3 3.1 - - - -
56B TYR* 2.9 75.3 + - + +
59B THR* 5.2 1.6 + - - -
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Residues in contact with THR 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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37B VAL* 4.1 6.8 + - + +
38B THR* 1.3 72.0 - - - +
40B VAL* 1.3 67.3 + - - +
53B GLU* 5.0 15.0 - - + +
54B VAL 3.3 7.4 - - - +
55B SER* 2.7 31.4 - - - +
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Residues in contact with VAL 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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38B THR* 4.1 18.2 - - + -
39B THR* 1.3 79.9 - - - +
41B VAL* 1.3 61.6 + - - +
42B ALA* 4.6 2.7 - - + -
52B GLN 3.6 0.2 - - - +
53B GLU* 3.3 3.7 - - - -
54B VAL* 2.6 55.6 + - + +
56B TYR* 4.2 9.9 - - + +
116B PHE* 3.8 54.5 - - + -
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Residues in contact with VAL 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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40B VAL* 1.3 76.2 - - - +
42B ALA* 1.3 59.5 + - - +
51B PRO* 3.7 27.4 - - + -
52B GLN* 3.3 9.4 - - - +
53B GLU* 4.3 19.3 - - + -
116B PHE* 3.4 14.6 - - - +
117B TYR 5.0 0.9 + - - -
503B K 4.0 8.7 - - - -
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Residues in contact with ALA 42 (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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40B VAL* 3.8 4.4 + - + -
41B VAL* 1.3 75.1 - - - +
43B THR* 1.3 62.5 + - - +
44B PRO* 3.8 0.2 - - - +
51B PRO* 3.6 1.5 - - - +
52B GLN* 2.9 39.0 + - - +
54B VAL* 4.1 12.8 - - + +
114B TYR* 3.7 22.8 - - + -
115B PHE 3.4 14.8 - - - +
116B PHE* 3.7 16.8 - - + -
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Residues in contact with THR 43 (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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42B ALA* 1.3 71.4 - - - +
44B PRO* 1.3 84.1 - - + +
49B ASP* 3.5 28.4 + - - +
50B ARG 3.8 11.2 - - - +
51B PRO* 3.8 15.4 - - - +
102B ARG* 4.0 8.3 - - - +
114B TYR* 3.3 2.0 - - - -
115B PHE* 3.0 49.1 + - + -
503B K 3.5 16.6 - - - -
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Residues in contact with PRO 44 (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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42B ALA 3.8 5.2 - - - +
43B THR* 1.3 97.0 - - + +
45B GLY* 1.3 64.6 + - - +
46B GLN 3.4 0.7 + - - -
47B GLY* 3.8 23.6 - - - +
48B PRO* 3.5 21.8 - - + +
50B ARG* 3.3 20.4 - - + +
52B GLN* 4.4 12.3 - - - +
102B ARG* 4.0 4.9 + - - -
113B ARG 3.5 10.5 - - - +
114B TYR* 3.7 14.1 - - + -
115B PHE* 4.1 0.3 - - - -
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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