Contacts of the strand formed by residues 38 - 44 (chain C) 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 THR 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C LYS* 4.1 7.2 + - - +
37C VAL* 1.3 76.4 + - - +
39C THR* 1.3 62.1 + - - +
40C VAL* 4.1 12.3 - - + -
55C SER* 3.3 2.6 - - - -
56C TYR* 2.9 74.5 + - + +
59C THR* 5.3 1.6 + - - -
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Residues in contact with THR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 4.1 7.4 + - + +
38C THR* 1.3 74.5 - - - +
40C VAL* 1.3 68.4 + - - +
53C GLU* 4.6 21.5 - - + +
54C VAL 3.3 7.9 - - - +
55C SER* 2.8 27.6 - - - +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C THR* 4.1 16.8 - - + -
39C THR* 1.3 80.1 - - - +
41C VAL* 1.3 62.5 + - - +
42C ALA* 3.7 2.4 + - + -
52C GLN 3.6 0.2 - - - +
53C GLU* 3.3 4.2 - - - -
54C VAL* 2.7 55.0 + - + +
56C TYR* 4.2 10.1 - - + +
116C PHE* 3.8 55.4 - - + -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 1.3 75.2 - - - +
42C ALA* 1.3 60.4 + - - +
51C PRO* 3.7 26.9 - - + -
52C GLN* 3.3 9.9 - - - +
53C GLU* 4.3 18.8 - - + -
116C PHE* 3.4 14.0 - - - +
117C TYR 5.0 0.7 + - - -
503C K 3.9 8.0 - - - -
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.7 4.4 + - + -
41C VAL* 1.3 74.1 - - - +
43C THR* 1.3 61.6 + - - +
44C PRO* 3.8 0.3 - - - +
51C PRO* 3.6 1.3 - - - +
52C GLN* 2.9 38.5 + - - +
54C VAL* 4.1 12.9 - - + +
114C TYR* 3.7 22.6 - - + -
115C PHE 3.4 16.2 - - - +
116C PHE* 3.7 16.6 - - + -
503C K 4.5 0.9 - - - -
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA* 1.3 71.9 - - - +
44C PRO* 1.3 86.0 - - + +
49C ASP* 3.5 28.1 + - - +
50C ARG 3.8 11.0 - - - +
51C PRO* 3.8 16.6 - - - +
102C ARG* 4.0 9.0 - - - +
114C TYR* 3.2 1.9 - - - -
115C PHE* 3.0 48.8 + - + -
503C K 3.5 15.2 - - - -
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Residues in contact with PRO 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA 3.8 4.9 - - - +
43C THR* 1.3 96.0 - - + +
45C GLY* 1.3 64.3 - - - +
46C GLN 3.4 0.6 + - - -
47C GLY* 3.8 24.7 - - - +
48C PRO* 3.5 21.5 - - + +
50C ARG* 3.0 21.5 - - + +
52C GLN* 3.9 15.5 - - - +
102C ARG* 4.0 5.0 + - - -
113C ARG 3.5 9.0 - - - +
114C TYR* 3.7 15.0 - - + -
115C PHE* 4.1 0.6 - - - -
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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