Contacts of the helix formed by residues 30 - 40 (chain C) in PDB entry 7CR3
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 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C THR* 1.3 72.5 - - - +
31C LYS* 1.3 82.8 + - + +
33C LEU* 3.3 14.7 + - - +
34C GLY 3.0 21.1 + - - -
46C GLU* 4.7 3.7 + - - +
49C LEU* 3.1 32.6 - - - +
50C GLN* 4.2 2.6 + - - +
53C ILE* 3.6 21.7 - - + +
62C GLY 4.3 9.2 + - - +
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Residues in contact with LYS 31 (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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29C THR* 3.2 9.9 - - - +
30C THR* 1.3 93.0 - - + +
32C GLU* 1.3 60.3 + - + +
34C GLY* 3.1 2.7 + - - +
35C THR* 2.9 31.0 + - - +
46C GLU* 2.4 43.9 + - - -
49C LEU* 4.8 7.0 - - - +
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Residues in contact with GLU 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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20C PHE* 2.9 28.1 - - - +
21C ASP* 2.8 15.5 - - - +
22C LYS* 2.4 35.7 + - + -
23C ASP* 3.1 16.5 - - - +
27C THR 4.4 0.4 - - - +
28C ILE* 3.2 28.6 - - + +
29C THR* 3.4 22.6 + - - +
30C THR 3.3 0.2 - - - -
31C LYS* 1.3 78.1 - - + +
33C LEU* 1.3 62.5 + - - +
35C THR* 3.2 10.9 - - - +
36C VAL* 3.0 29.5 + - - +
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Residues in contact with LEU 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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543B VAL* 5.6 1.2 - - - +
546B MET* 4.5 5.6 - - - -
20C PHE* 3.7 19.7 - - + -
28C ILE* 3.6 25.6 - - + -
29C THR 3.3 10.3 - - - +
30C THR* 3.4 17.3 - - - +
31C LYS 3.3 0.2 - - - -
32C GLU* 1.3 76.5 - - - +
34C GLY* 1.3 63.0 + - - +
36C VAL* 3.1 8.7 - - - +
37C MET* 3.0 25.6 + - - +
49C LEU* 3.8 34.4 - - + +
52C MET* 4.5 11.7 - - + -
53C ILE* 4.1 4.0 - - + -
64C ILE* 3.6 28.9 - - + -
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Residues in contact with GLY 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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30C THR 3.0 11.9 + - - -
31C LYS* 3.1 4.8 + - - -
33C LEU* 1.3 77.7 - - - +
35C THR* 1.3 56.6 + - - +
37C MET* 3.5 2.3 + - - +
38C ARG* 2.9 37.0 + - - +
44C PRO* 4.2 5.6 - - - +
49C LEU* 3.5 24.6 - - - +
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Residues in contact with THR 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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22C LYS* 3.3 29.9 + - + +
31C LYS 2.9 16.0 + - - +
32C GLU* 3.2 21.1 - - - +
34C GLY* 1.3 76.2 - - - +
36C VAL* 1.3 58.1 + - - +
38C ARG* 3.7 11.5 - - - +
39C SER* 2.9 25.1 + - - -
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Residues in contact with VAL 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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543B VAL* 5.3 9.2 - - + -
19C LEU* 4.3 10.1 - - + +
20C PHE* 4.6 29.4 - - + -
22C LYS* 3.9 27.1 - - - +
32C GLU 3.0 23.9 + - - +
33C LEU* 3.1 18.6 - - - +
35C THR* 1.3 74.6 - - - +
37C MET* 1.3 65.8 + - - +
38C ARG 3.3 0.2 - - - -
39C SER* 3.1 21.7 + - - -
40C LEU* 3.3 9.4 + - - +
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Residues in contact with MET 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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543B VAL* 4.1 23.3 - - + -
547B ARG* 4.2 27.6 - - - +
33C LEU 3.0 18.1 + - - +
34C GLY 3.8 0.2 - - - +
36C VAL* 1.3 78.6 - - - +
38C ARG* 1.3 59.4 + - - +
40C LEU* 3.2 45.4 + - + +
41C GLY 3.3 0.3 + - - -
42C GLN* 2.9 56.7 + - + +
44C PRO* 3.6 20.2 - - + -
49C LEU* 5.1 2.0 - - + -
52C MET* 5.5 4.0 - - + -
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Residues in contact with ARG 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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34C GLY 2.9 25.3 + - - +
35C THR* 3.7 10.3 - - - +
37C MET* 1.3 76.1 - - - +
39C SER* 1.3 58.6 + - - +
40C LEU 3.0 0.2 - - - -
41C GLY* 2.9 19.1 + - - +
42C GLN 3.2 13.9 - - - +
43C ASN* 4.1 31.5 - - - +
44C PRO* 4.2 11.3 + - + +
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Residues in contact with SER 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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367B VAL* 5.2 7.3 - - - +
22C LYS* 6.1 1.3 - - - -
35C THR 2.9 17.4 + - - -
36C VAL* 3.1 19.2 + - - -
38C ARG* 1.3 75.5 - - - +
40C LEU* 1.3 56.8 + - - +
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Residues in contact with LEU 40 (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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363B TYR* 3.5 44.4 - - + +
366B THR* 2.7 32.6 - - - +
367B VAL* 3.4 15.5 - - + +
540B ILE* 3.8 31.4 - - + -
543B VAL* 5.4 3.1 - - + -
547B ARG* 5.2 5.2 - - - +
36C VAL 3.3 7.2 + - - +
37C MET* 3.2 34.3 + - + +
38C ARG 3.0 0.8 - - - -
39C SER* 1.3 77.0 - - - +
41C GLY* 1.3 52.2 + - - +
42C GLN* 3.7 2.7 - - + +
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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