Contacts of the strand formed by residues 38 - 44 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D LYS* 4.1 6.8 + - - +
37D VAL* 1.3 75.7 + - - +
39D THR* 1.3 64.8 + - - +
40D VAL* 4.1 12.3 - - + -
55D SER* 3.2 3.6 - - - -
56D TYR* 2.9 75.0 + - + +
59D THR* 5.3 1.0 + - - -
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Residues in contact with THR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 4.1 5.9 + - + +
38D THR* 1.3 74.4 - - - +
40D VAL* 1.3 67.7 + - - +
53D GLU* 5.0 15.5 - - + +
54D VAL 3.3 7.4 - - - +
55D SER* 2.7 31.0 - - - +
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D THR* 4.1 17.5 - - + -
39D THR* 1.3 81.4 - - - +
41D VAL* 1.3 62.0 + - - +
42D ALA* 3.7 2.6 + - + -
52D GLN 3.6 0.2 - - - +
53D GLU* 3.3 4.2 - - - -
54D VAL* 2.7 53.4 + - + +
56D TYR* 4.2 10.8 - - + +
116D PHE* 3.8 55.2 - - + -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 1.3 76.5 - - - +
42D ALA* 1.3 59.0 + - - +
51D PRO* 3.7 26.9 - - + -
52D GLN* 3.3 9.2 - - - +
53D GLU* 4.4 18.4 - - + +
116D PHE* 3.4 13.9 - - - +
117D TYR 5.0 1.0 + - - -
503D K 4.0 8.7 - - - -
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D VAL* 3.7 4.0 + - + -
41D VAL* 1.3 75.6 - - - +
43D THR* 1.3 62.7 + - - +
44D PRO* 3.8 0.2 - - - +
51D PRO* 4.1 1.6 - - - -
52D GLN* 2.9 37.5 + - - +
54D VAL* 4.1 12.9 - - + +
114D TYR* 3.7 22.2 - - + -
115D PHE 3.4 15.0 - - - +
116D PHE* 3.7 17.0 - - + -
131D VAL* 5.9 0.2 - - + -
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 1.3 71.6 - - - +
44D PRO* 1.3 85.5 - - + +
49D ASP* 3.5 27.7 + - - +
50D ARG 3.8 11.2 - - - +
51D PRO* 3.8 16.7 - - - +
102D ARG* 4.1 3.1 - - - +
114D TYR* 3.2 1.7 - - - -
115D PHE* 3.0 54.3 + - + -
503D K 3.5 15.0 - - - -
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Residues in contact with PRO 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA 3.8 5.6 - - - +
43D THR* 1.3 96.7 - - + +
45D GLY* 1.3 64.2 + - - +
46D GLN 4.6 0.2 - - - +
47D GLY* 3.9 23.6 - - - +
48D PRO* 3.5 21.3 - - + +
50D ARG* 3.3 20.9 - - + +
52D GLN* 4.2 13.7 - - - +
102D ARG* 4.0 4.9 + - - -
113D ARG 3.5 9.9 - - - +
114D TYR* 3.6 13.9 - - + -
115D PHE* 4.1 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