Contacts of the helix formed by residues 49 - 59 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ARG* 4.7 1.2 + - - -
28D PHE* 3.6 8.7 - - - +
29D SER 3.5 0.9 - - - +
30D GLU 3.4 20.9 - - - +
31D PRO* 3.2 28.4 - - + +
32D VAL 5.3 0.2 - - - +
48D MET* 1.3 81.1 - - - +
50D PHE* 1.3 64.2 + - - +
51D PHE* 2.8 33.3 + - - +
52D THR* 2.5 29.1 + - - -
53D MET* 3.1 21.7 + - - +
75D ILE* 3.6 13.0 - - - -
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Residues in contact with PHE 50 (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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16D LEU* 3.6 22.9 - - + +
19D LEU* 3.9 35.9 - - + -
20D GLN* 3.7 39.3 + - + +
23D ASP* 4.0 15.0 - - + -
28D PHE* 2.9 45.0 + - + +
29D SER* 4.2 8.3 - - - +
49D ASP* 1.3 69.3 - - - +
51D PHE* 1.3 59.8 + - - +
53D MET* 3.7 6.0 - - - +
54D LYS* 3.0 26.5 + - - +
72D PHE* 4.2 10.8 - + - -
75D ILE* 3.8 17.3 - - + -
96D LEU* 4.2 17.3 - - + -
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Residues in contact with PHE 51 (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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51A PHE* 6.2 0.7 - + - -
55A GLN* 3.5 28.5 - - + -
20D GLN* 5.9 0.4 - - - +
29D SER 3.1 17.1 + - - +
30D GLU* 3.6 24.2 - - - +
31D PRO* 5.0 5.8 - - + -
49D ASP* 2.8 14.8 + - - +
50D PHE* 1.3 67.5 - - - +
52D THR* 1.3 73.3 + - - +
54D LYS* 3.2 5.4 + - + +
55D GLN* 3.0 57.6 + - + +
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Residues in contact with THR 52 (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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59A ALA* 5.0 0.2 - - - +
61A ARG* 3.1 38.1 + - - +
31D PRO* 4.2 4.7 - - - +
47D PRO 5.7 0.2 - - - +
48D MET* 3.7 24.7 - - + -
49D ASP* 2.5 33.4 + - - -
51D PHE* 1.3 81.3 - - - +
53D MET* 1.3 56.0 + - - +
55D GLN* 3.1 8.1 + - + +
56D ASN* 2.9 40.2 + - - +
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Residues in contact with MET 53 (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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16D LEU* 4.2 12.7 - - + +
19D LEU* 5.3 0.7 - - + -
48D MET* 3.8 11.9 - - - -
49D ASP 3.1 15.8 + - - +
50D PHE* 3.7 17.0 - - - +
51D PHE 3.3 0.2 - - - -
52D THR* 1.3 75.8 - - - +
54D LYS* 1.3 62.6 + - - +
56D ASN 3.3 0.5 + - - -
57D LEU* 2.9 23.9 + - - +
62D TYR* 3.5 26.0 - - + +
68D PHE* 3.5 57.7 - - + +
71D ASP* 4.0 1.3 - - + -
72D PHE* 3.8 20.0 - - + +
75D ILE* 3.7 24.5 - - - -
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Residues in contact with LYS 54 (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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13D ARG* 3.9 20.4 - - - +
16D LEU* 3.8 21.7 - - + +
20D GLN* 5.4 4.3 - - - +
50D PHE 3.0 13.8 + - - +
51D PHE* 3.2 11.2 + - + +
53D MET* 1.3 76.2 - - - +
55D GLN* 1.3 73.8 + - - +
57D LEU* 3.3 6.4 + - + +
58D GLU* 2.6 61.5 + - + +
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Residues in contact with GLN 55 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.5 29.1 - - + -
55A GLN* 4.4 17.9 - - + -
61A ARG* 6.3 0.7 - - - +
51D PHE* 3.0 62.0 + - + +
52D THR* 3.1 7.8 + - + +
54D LYS* 1.3 89.6 - - - +
56D ASN* 1.3 64.3 + - - +
58D GLU* 3.4 8.2 + - - +
59D ALA* 3.0 26.2 + - - +
61D ARG* 3.6 11.7 + - - +
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Residues in contact with ASN 56 (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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48D MET* 4.4 3.4 - - - +
52D THR* 2.9 33.3 + - - +
53D MET 3.6 1.8 - - - +
54D LYS 3.3 0.2 - - - -
55D GLN* 1.3 77.0 - - - +
57D LEU* 1.3 63.3 + - - +
59D ALA 3.3 1.6 + - - -
60D TYR 3.2 2.9 + - - -
61D ARG* 2.9 69.9 + - + +
62D TYR* 3.0 40.3 + - + +
71D ASP* 3.5 10.3 + - - -
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Residues in contact with LEU 57 (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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9D LEU* 3.7 24.9 - - + +
12D LEU* 3.4 49.1 - - + +
13D ARG* 3.5 25.8 - - + +
16D LEU* 4.1 18.2 - - + -
53D MET 2.9 13.0 + - - +
54D LYS* 3.4 11.0 - - + +
56D ASN* 1.3 75.8 - - - +
58D GLU* 1.3 77.9 + - - +
60D TYR* 3.0 20.6 + - - -
62D TYR* 3.8 14.5 - - + -
68D PHE* 4.6 3.6 - - + -
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Residues in contact with GLU 58 (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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2D PRO 4.7 8.5 - - - +
3D LEU* 4.2 10.2 - - - +
4D GLN* 3.5 21.3 + - - +
9D LEU* 5.1 1.3 - - - +
13D ARG* 2.8 38.5 + - - +
54D LYS* 2.6 54.6 + - + +
55D GLN* 4.0 8.3 - - - +
57D LEU* 1.3 79.9 - - - +
59D ALA* 1.3 58.6 + - - +
60D TYR 3.2 1.5 + - - -
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Residues in contact with ALA 59 (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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31A PRO* 3.9 33.3 - - + +
32A VAL 5.0 1.7 - - - +
34A LEU* 4.8 5.2 - - - +
4D GLN* 4.5 4.4 + - - +
55D GLN 3.0 16.0 + - - +
56D ASN 3.8 2.0 - - - +
57D LEU 3.3 0.2 - - - -
58D GLU* 1.3 74.5 - - - +
60D TYR* 1.3 68.6 + - - +
61D ARG* 3.2 38.0 + - + +
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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