Contacts of the helix formed by residues 49 - 62 (chain C) in PDB entry 7CE1
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 GLU 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C GLY* 3.0 1.4 + - - -
48C ALA* 1.3 80.1 + - + +
50C THR* 1.3 67.9 + - - +
51C LYS 2.9 0.7 - - - -
52C GLU* 3.2 16.5 - - + +
53C ARG* 2.5 36.9 + - + +
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Residues in contact with THR 50 (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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31C LEU* 4.7 12.8 - - + -
35C THR* 5.7 0.7 - - - -
46C ILE* 3.8 8.8 - - - +
47C GLY* 2.8 35.6 + - - -
49C GLU* 1.3 85.8 + - - +
51C LYS* 1.3 62.5 + - - +
53C ARG* 3.4 32.5 + - - +
54C VAL* 3.0 32.0 + - - +
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Residues in contact with LYS 51 (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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39C ALA* 4.4 24.4 - - - +
42C ASP* 2.6 43.4 + - - +
43C ALA 2.8 32.0 + - - +
44C PRO* 5.0 1.2 - - - +
46C ILE* 3.6 26.9 - - + +
47C GLY 2.9 15.6 + - - +
48C ALA* 3.3 15.5 - - - +
50C THR* 1.3 79.1 + - - +
52C GLU* 1.3 56.2 + - - +
54C VAL* 3.3 2.1 + - - +
55C ARG* 3.0 31.7 + - - +
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Residues in contact with GLU 52 (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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48C ALA 3.6 3.3 + - - +
49C GLU* 3.1 25.3 + - + +
51C LYS* 1.3 78.1 - - - +
53C ARG* 1.3 64.1 + - - +
55C ARG* 4.7 9.2 - - - +
56C LEU* 3.1 37.1 + - + +
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Residues in contact with ARG 53 (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* 3.7 33.5 + - + +
31C LEU* 4.0 23.1 - - - +
49C GLU* 2.5 23.9 + - + +
50C THR* 3.6 31.8 - - - +
51C LYS 3.2 0.2 - - - -
52C GLU* 1.3 74.5 - - - +
54C VAL* 1.3 65.1 + - + +
56C LEU* 3.9 4.9 - - - +
57C ILE* 3.1 25.7 + - - +
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Residues in contact with VAL 54 (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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25C ILE* 4.2 6.3 - - + -
29C THR* 4.8 6.7 - - + -
31C LEU* 4.1 22.7 - - + -
35C THR* 5.5 0.9 - - + -
36C VAL* 3.6 37.0 - - + -
39C ALA* 3.8 23.3 - - + -
40C LEU* 3.8 13.9 - - + -
50C THR 3.0 17.5 + - - +
51C LYS 3.9 0.7 - - - +
53C ARG* 1.3 76.0 - - + +
55C ARG* 1.3 61.2 + - - +
57C ILE* 3.1 9.7 - - - +
58C ALA* 2.9 27.6 + - + +
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Residues in contact with ARG 55 (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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39C ALA 5.6 4.0 - - - +
40C LEU* 3.4 50.6 + - + +
51C LYS 3.0 16.3 + - - +
52C GLU* 4.7 9.6 - - - +
54C VAL* 1.3 78.0 - - - +
56C LEU* 1.3 62.1 + - - +
58C ALA* 3.8 5.1 - - - +
59C GLN* 3.1 30.0 + - + +
63C TYR* 5.7 4.9 + - - -
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Residues in contact with LEU 56 (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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52C GLU* 3.1 31.5 + - + +
53C ARG* 3.9 3.8 - - - +
54C VAL 3.2 0.8 - - - -
55C ARG* 1.3 77.0 - - - +
57C ILE* 1.3 71.4 + - + +
59C GLN* 3.5 5.5 + - - +
60C GLN* 3.1 43.2 + - + +
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Residues in contact with ILE 57 (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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25C ILE* 4.1 17.5 - - + +
28C MET* 3.7 43.5 - - + -
29C THR* 4.2 15.3 - - + -
53C ARG 3.1 16.7 + - - +
54C VAL* 3.1 24.7 - - - +
56C LEU* 1.3 79.6 - - + +
58C ALA* 1.3 64.5 + - - +
60C GLN* 3.2 4.8 + - + +
61C ILE* 3.1 33.3 + - + +
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Residues in contact with ALA 58 (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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25C ILE* 4.1 18.8 - - + -
40C LEU* 3.8 22.7 - - + -
54C VAL 2.9 19.3 + - - +
55C ARG* 3.8 10.1 - - - +
56C LEU 3.2 0.2 - - - -
57C ILE* 1.3 77.5 - - - +
59C GLN* 1.3 57.1 + - - +
61C ILE* 3.6 5.7 - - - +
62C GLY 2.9 24.4 + - - -
63C TYR* 2.9 19.7 + - + +
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Residues in contact with GLN 59 (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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55C ARG* 3.1 22.3 + - + +
56C LEU* 4.0 5.6 - - - +
58C ALA* 1.3 79.3 - - - +
60C GLN* 1.3 69.6 + - + +
62C GLY* 3.6 11.5 + - - -
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Residues in contact with GLN 60 (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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56C LEU* 3.1 33.7 + - + +
57C ILE* 3.7 7.0 - - + +
58C ALA 3.1 1.0 - - - -
59C GLN* 1.3 88.5 - - + +
61C ILE* 1.3 61.1 + - + +
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Residues in contact with ILE 61 (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 PRO* 3.8 34.4 - - + +
25C ILE* 3.9 26.0 - - + +
28C MET* 4.6 24.5 - - + -
57C ILE* 3.1 29.3 + - + +
58C ALA 3.6 4.3 - - - +
60C GLN* 1.3 77.4 - - + +
62C GLY* 1.3 63.2 + - - +
63C TYR* 4.2 3.8 - - + +
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Residues in contact with GLY 62 (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 PRO* 4.5 5.9 - - - +
58C ALA 2.9 7.3 + - - -
59C GLN* 3.8 10.3 - - - -
60C GLN 3.4 1.2 - - - -
61C ILE* 1.3 80.7 - - - +
63C TYR* 1.3 65.0 - - - +
64C GLN* 3.4 8.3 + - - +
132D GLU* 5.7 1.0 - - - +
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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