Contacts of the strand formed by residues 31 - 38 (chain C) in PDB entry 5J7C
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 TYR 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 5.6 0.2 - - - -
48A ASP* 2.9 30.1 + - - -
50A SER* 3.1 16.8 + - - -
59A ASN* 3.2 21.7 + - + -
61A ARG* 3.6 13.6 - - - +
62A TRP* 3.7 23.1 - + - -
29C ALA* 4.1 2.4 - - - +
30C THR* 1.3 97.5 + - - +
32C TYR* 1.3 75.5 + - - +
48C PHE* 4.0 13.5 - + + -
49C THR* 3.2 31.4 - - - +
50C MET 4.1 6.3 - - - -
51C PRO* 4.1 11.7 - - + -
75C ALA* 3.7 1.7 - - - -
76C VAL* 2.8 37.1 + - + +
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Residues in contact with TYR 32 (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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23C TRP* 3.6 47.1 - + + +
24C ARG 4.7 2.2 - - - -
25C GLY* 3.2 9.9 - - - -
26C TYR* 2.9 31.8 + + - -
29C ALA* 3.4 27.9 - - + +
31C TYR* 1.3 81.0 - - - +
33C GLY* 1.3 59.5 + - - +
34C ILE* 4.8 0.9 - - + -
48C PHE* 3.2 8.4 - - - +
49C THR* 2.9 43.9 + - + +
53C ASP 4.9 8.7 - - - -
54C LEU* 5.7 3.0 - - + +
56C HIS* 3.7 15.8 + + - -
73C VAL* 4.3 8.3 - - + -
74C TYR 3.3 8.3 - - - +
75C ALA* 3.7 22.7 - - + -
76C VAL* 4.4 0.9 - - - +
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Residues in contact with GLY 33 (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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32C TYR* 1.3 73.4 - - - +
34C ILE* 1.3 62.4 + - - +
35C ILE* 5.0 0.2 - - - -
46C GLN* 5.1 0.4 - - - -
47C GLU 3.3 8.3 - - - -
48C PHE* 3.7 14.5 - - - -
72C THR 3.6 1.4 - - - +
73C VAL* 3.3 6.6 - - - -
74C TYR* 2.9 52.4 + - - -
76C VAL* 4.3 2.8 - - - +
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Residues in contact with ILE 34 (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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21C ILE* 3.8 19.7 - - + -
23C TRP* 4.0 24.2 - - + -
32C TYR* 4.8 1.1 - - + -
33C GLY* 1.3 77.5 - - - +
35C ILE* 1.3 62.9 + - - +
36C TYR* 4.3 6.6 + - + -
45C VAL 3.5 1.2 - - - +
46C GLN* 3.2 3.8 - - - -
47C GLU* 2.7 52.0 + - + +
48C PHE 5.5 0.2 - - - -
49C THR* 4.6 13.9 - - + -
58C ALA* 4.9 7.4 - - + -
60C ILE* 3.8 21.8 - - + -
71C ILE* 4.4 4.3 - - + -
72C THR 3.4 5.4 - - - +
73C VAL* 3.6 28.5 - - + -
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Residues in contact with ILE 35 (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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34C ILE* 1.3 76.6 - - - +
36C TYR* 1.3 63.4 + - - +
44C LEU* 3.7 32.1 - - + -
45C VAL 3.2 8.1 - - - +
46C GLN* 3.5 32.8 - - + +
70C THR 3.5 1.9 - - - +
71C ILE* 3.4 2.9 - - - +
72C THR* 2.7 55.5 + - + +
74C TYR* 3.9 18.6 - - + -
44D LEU* 4.4 18.2 - - + -
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Residues in contact with TYR 36 (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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34C ILE* 4.5 7.4 - - + -
35C ILE* 1.3 79.3 - - - +
37C GLY* 1.3 60.5 + - - +
44C LEU* 3.6 4.2 - - - -
45C VAL* 2.9 68.4 + - + +
47C GLU* 3.1 31.6 + - + -
60C ILE* 3.6 54.7 - - + +
61C SER 4.2 9.3 + - - -
63C LEU* 3.9 19.5 - - + -
69C TYR* 5.0 6.3 - + + -
70C THR 3.2 9.6 - - - +
71C ILE* 4.5 8.3 - - + -
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Residues in contact with GLY 37 (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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36C TYR* 1.3 78.6 - - - +
38C GLU* 1.3 66.2 + - - -
43C SER 4.1 14.4 - - - -
44C LEU* 4.5 7.9 - - - +
69C TYR* 3.4 13.0 - - - -
70C THR* 2.8 32.6 + - - +
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Residues in contact with GLU 38 (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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70B PRO* 3.5 37.4 - - + +
37C GLY* 1.3 72.6 - - - -
39C THR* 1.3 58.3 + - - +
40C GLY 3.1 0.9 + - - -
41C GLY* 2.6 34.7 + - - +
43C SER 4.6 5.0 + - - +
44C LEU* 6.1 0.7 - - - +
64C LYS* 6.1 1.2 - - - +
67C VAL* 3.2 35.5 - - + +
68C ASP 3.4 8.2 + - - +
69C TYR* 3.5 11.7 - - + -
46D GLN* 4.5 2.8 + - - -
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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