Contacts of the helix formed by residues 49 - 59 (chain C) in PDB entry 4QYL
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 ASP 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ARG* 4.6 1.0 + - - -
28C PHE* 3.6 9.0 - - - +
29C SER 3.5 1.0 - - - +
30C GLU 3.4 20.6 - - - +
31C PRO* 3.3 28.4 - - + +
32C VAL 5.3 0.2 - - - +
47C PRO 5.7 0.2 - - - -
48C MET* 1.3 80.6 - - - +
50C PHE* 1.3 64.1 + - - +
51C PHE* 2.9 33.1 + - - +
52C THR* 2.5 30.0 + - - -
53C MET* 3.1 22.3 + - - +
75C ILE* 3.7 12.8 - - - -
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Residues in contact with PHE 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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16C LEU* 3.6 22.9 - - + +
19C LEU* 3.9 35.7 - - + -
20C GLN* 3.8 37.7 + - + +
23C ASP* 4.0 15.7 - - + -
28C PHE* 2.9 46.7 + - + +
29C SER* 4.2 7.6 - - - +
49C ASP* 1.3 70.8 - - - +
51C PHE* 1.3 61.1 + - - +
53C MET* 3.7 5.4 - - - +
54C LYS* 3.0 26.5 + - - +
72C PHE* 4.1 11.0 - + - -
75C ILE* 3.9 17.5 - - + -
96C LEU* 4.2 16.4 - - + -
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Residues in contact with PHE 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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51B PHE* 6.4 0.2 - + - -
55B GLN* 3.5 28.9 - - + -
20C GLN* 5.9 0.2 - - - +
29C SER 3.1 17.0 + - - +
30C GLU* 3.6 23.3 - - - +
31C PRO* 5.0 5.6 - - + -
49C ASP* 2.9 11.0 + - - +
50C PHE* 1.3 72.6 - - - +
52C THR* 1.3 69.9 + - - +
54C LYS* 3.2 5.4 + - + +
55C GLN* 3.0 58.3 + - + +
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Residues in contact with THR 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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59B ALA* 5.0 0.2 - - - +
61B ARG* 3.1 38.5 + - - +
31C PRO* 4.2 4.3 - - - +
47C PRO 5.7 0.2 - - - +
48C MET* 3.7 23.8 - - + -
49C ASP* 2.5 33.8 + - - -
51C PHE* 1.3 78.9 - - - +
53C MET* 1.3 61.9 + - - +
55C GLN* 3.1 8.8 + - + +
56C ASN* 2.9 35.7 + - - +
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Residues in contact with MET 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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16C LEU* 4.1 12.3 - - + -
19C LEU* 5.4 0.7 - - + -
48C MET* 3.8 11.9 - - - -
49C ASP 3.1 16.8 + - - +
50C PHE* 3.7 17.9 - - - +
51C PHE 3.3 0.2 - - - -
52C THR* 1.3 75.0 - - - +
54C LYS* 1.3 64.4 + - - +
56C ASN 3.3 0.5 + - - -
57C LEU* 2.9 21.7 + - - +
62C TYR* 3.4 26.9 - - - +
68C PHE* 3.5 57.0 - - + +
71C ASP* 4.0 1.6 - - + -
72C PHE* 3.8 19.5 - - + +
75C ILE* 3.6 24.9 - - - -
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Residues in contact with LYS 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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13C ARG* 3.9 20.2 - - - +
16C LEU* 3.8 22.4 - - + +
17C GLU* 5.1 8.8 + - - +
20C GLN* 5.4 3.8 - - - +
50C PHE 3.0 14.6 + - - +
51C PHE* 3.2 10.7 + - + +
53C MET* 1.3 76.7 - - - +
55C GLN* 1.3 73.9 + - - +
57C LEU* 3.4 6.5 + - + +
58C GLU* 2.6 57.3 + - + +
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Residues in contact with GLN 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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51B PHE* 3.5 28.4 - - + -
55B GLN* 4.3 18.2 - - + -
61B ARG* 6.2 1.3 - - - +
51C PHE* 3.0 67.8 + - + +
52C THR* 3.1 7.6 + - + +
54C LYS* 1.3 89.0 - - - +
56C ASN* 1.3 56.2 + - - +
58C GLU* 3.4 8.1 + - - +
59C ALA* 3.0 31.7 + - - +
61C ARG* 3.6 11.7 + - - +
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Residues in contact with ASN 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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48C MET* 4.4 3.4 - - - +
52C THR* 2.9 36.1 + - - +
55C GLN* 1.3 72.8 - - - +
57C LEU* 1.3 66.5 + - - +
59C ALA 3.3 2.1 + - - -
60C TYR 3.2 2.9 + - - -
61C ARG* 2.9 63.0 + - + +
62C TYR* 3.0 40.8 + - + +
71C ASP* 3.4 10.3 + - - -
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Residues in contact with LEU 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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9C LEU* 3.8 25.7 - - + +
12C LEU* 3.5 48.0 - - + +
13C ARG* 3.6 25.6 - - + +
16C LEU* 4.1 18.4 - - + -
53C MET 2.9 12.6 + - - +
54C LYS* 3.4 11.0 - - + +
56C ASN* 1.3 75.2 - - - +
58C GLU* 1.3 76.8 + - - +
60C TYR* 3.0 20.6 + - - -
62C TYR* 3.7 15.5 - - + -
68C PHE* 4.5 4.0 - - + -
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Residues in contact with GLU 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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31B PRO* 5.6 0.3 - - - +
2C PRO* 4.7 8.9 - - - +
3C LEU* 4.2 9.7 - - - +
4C GLN* 3.6 21.0 + - - +
9C LEU* 5.3 1.3 - - - +
13C ARG* 2.8 38.6 + - - +
54C LYS* 2.6 59.5 + - + +
55C GLN* 4.0 8.3 - - - +
57C LEU* 1.3 81.2 - - - +
59C ALA* 1.4 59.0 + - - +
60C TYR 3.2 1.5 + - - -
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Residues in contact with ALA 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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31B PRO* 3.8 33.3 - - + +
32B VAL 5.0 1.9 - - - +
34B LEU* 4.9 4.7 - - - +
52B THR* 4.9 0.2 - - - +
4C GLN* 4.5 3.6 + - - +
55C GLN 3.0 15.9 + - - +
56C ASN 3.3 2.2 + - - +
58C GLU* 1.4 76.1 - - - +
60C TYR* 1.3 66.4 + - - +
61C ARG* 3.2 38.2 + - + +
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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