Contacts of the helix formed by residues 49 - 59 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B PHE* 3.6 8.1 - - - +
29B SER 3.5 1.2 - - - +
30B GLU 3.4 21.3 - - - +
31B PRO* 3.3 27.9 - - + +
32B VAL 5.3 0.2 - - - +
48B MET* 1.3 82.5 - - - +
50B PHE* 1.3 63.3 + - - +
51B PHE* 2.8 33.1 + - - +
52B THR* 2.5 28.8 + - - -
53B MET* 3.1 22.0 + - - +
75B ILE* 3.6 13.0 - - - -
61C ARG* 4.6 1.2 + - - -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.6 23.7 - - + +
19B LEU* 3.9 37.2 - - + -
20B GLN* 3.8 32.6 + - + +
23B ASP* 4.0 21.1 - - + -
28B PHE* 2.9 45.7 + - + +
29B SER* 4.2 7.9 - - - +
49B ASP* 1.3 70.5 - - - +
51B PHE* 1.3 58.9 + - - +
53B MET* 3.5 7.3 + - - +
54B LYS* 3.0 27.4 + - - +
72B PHE* 4.2 9.9 - + - -
75B ILE* 3.8 16.8 - - + +
96B LEU* 4.2 17.5 - - + -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER 3.1 16.4 + - - +
30B GLU* 3.6 25.4 - - - +
31B PRO* 5.0 4.9 - - + -
49B ASP* 2.8 13.9 + - - +
50B PHE* 1.3 69.6 - - - +
52B THR* 1.3 68.2 + - - +
54B LYS* 3.2 5.8 + - + +
55B GLN* 3.1 58.0 + - + +
51C PHE* 6.4 0.2 - + - -
55C GLN* 3.5 28.5 - - + -
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Residues in contact with THR 52 (chain B).
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* 4.1 4.7 - - - +
47B PRO 5.6 0.4 - - - +
48B MET* 3.6 24.2 - - + -
49B ASP* 2.5 33.4 + - - -
51B PHE* 1.3 80.6 - - - +
53B MET* 1.3 56.0 + - - +
55B GLN* 3.1 9.2 + - + +
56B ASN* 2.9 40.2 + - - +
59C ALA* 4.9 0.2 - - - +
61C ARG* 3.1 38.5 + - - +
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Residues in contact with MET 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.2 11.2 - - + +
19B LEU* 5.4 0.4 - - + -
48B MET* 3.8 11.7 - - - -
49B ASP 3.1 15.7 + - - +
50B PHE* 3.7 17.7 - - - +
52B THR* 1.3 75.4 - - - +
54B LYS* 1.3 63.8 + - - +
56B ASN 3.3 0.3 + - - -
57B LEU* 2.9 24.3 + - - +
62B TYR* 3.5 26.7 - - - +
68B PHE* 3.5 56.8 - - + +
71B ASP* 4.0 1.6 - - + -
72B PHE* 3.8 20.0 - - + +
75B ILE* 3.6 25.1 - - - -
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Residues in contact with LYS 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.9 20.0 - - - +
16B LEU* 3.8 21.4 - - + +
20B GLN* 5.4 4.5 - - - +
50B PHE 3.0 15.1 + - - +
51B PHE* 3.2 10.7 + - + +
53B MET* 1.3 75.1 - - - +
55B GLN* 1.3 74.3 + - - +
57B LEU* 3.4 6.3 + - + +
58B GLU* 2.6 57.0 + - + +
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Residues in contact with GLN 55 (chain B).
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* 3.1 63.5 + - + +
52B THR* 3.1 6.7 + - + +
54B LYS* 1.3 88.6 - - - +
56B ASN* 1.3 63.8 - - - +
58B GLU* 3.4 7.9 + - - +
59B ALA* 3.0 26.2 + - - +
61B ARG* 3.7 12.2 + - - +
51C PHE* 3.5 29.7 - - + -
55C GLN* 4.3 17.7 - - + -
61C ARG* 6.2 1.3 - - - +
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B MET* 4.4 3.0 - - - +
52B THR* 2.9 33.8 + - - +
53B MET* 3.6 1.3 - - - +
54B LYS 3.3 0.2 - - - -
55B GLN* 1.3 73.9 - - - +
57B LEU* 1.3 65.7 + - - +
59B ALA 3.2 1.9 + - - -
60B TYR 3.2 3.5 + - - -
61B ARG* 2.9 68.5 + - + +
62B TYR* 3.1 39.7 + - + +
71B ASP* 3.5 10.1 + - - -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.7 25.7 - - + +
12B LEU* 3.5 48.5 - - + +
13B ARG* 3.6 25.1 - - + +
16B LEU* 4.1 18.2 - - + -
53B MET 2.9 12.6 + - - +
54B LYS* 3.4 11.7 - - + +
56B ASN* 1.3 76.6 - - - +
58B GLU* 1.4 78.2 + - - +
60B TYR* 3.0 21.3 + - - -
62B TYR* 3.7 14.4 + - + -
68B PHE* 4.5 4.0 - - + -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PRO* 4.6 10.7 - - - +
3B LEU* 4.2 10.3 - - - +
4B GLN* 3.6 21.1 + - - +
9B LEU* 5.2 1.4 - - - +
13B ARG* 2.9 38.7 + - - +
54B LYS* 2.6 55.4 + - + +
55B GLN* 4.0 8.5 - - - +
57B LEU* 1.4 79.6 - - - +
59B ALA* 1.3 58.7 + - - +
60B TYR 3.2 1.1 + - - -
31C PRO* 5.6 0.6 - - - +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLN* 4.7 3.1 + - - +
55B GLN 3.0 16.0 + - - +
56B ASN 3.2 2.4 + - - +
58B GLU* 1.3 73.9 - - - +
60B TYR* 1.3 68.2 + - - +
61B ARG* 3.2 38.2 + - + +
31C PRO* 3.9 33.5 - - + +
32C VAL 5.0 2.1 - - - +
34C LEU* 4.9 4.3 - - - +
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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