Contacts of the strand formed by residues 52 - 58 (chain D) in PDB entry 4LL4
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 VAL 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D LEU* 3.3 32.3 - - + +
24D VAL* 3.8 16.8 - - + -
46D SER 5.3 0.3 - - - +
49D TYR* 3.0 30.4 + - + +
50D SER* 4.0 6.9 - - - +
51D ASN* 1.3 84.8 - - - +
53D ILE* 1.3 66.5 + - - +
54D PHE* 3.4 25.9 - - + -
101D ILE* 4.4 4.9 - - + -
105D VAL* 3.7 30.3 - - + -
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Residues in contact with ILE 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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3D LYS* 6.1 0.7 - - + -
14D ALA* 5.5 4.7 - - + +
17D ALA 5.2 0.7 - - - +
18D ALA* 3.9 26.7 - - + +
21D LYS* 3.5 38.8 - - + +
22D LEU 2.7 14.0 + - - +
23D VAL* 3.1 16.3 - - + -
24D VAL* 2.6 35.7 + - - +
52D VAL* 1.3 76.7 - - - +
54D PHE* 1.3 58.5 + - - +
55D LEU* 3.8 22.9 - - + -
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Residues in contact with PHE 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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1D MET 4.0 8.5 + - - +
2D VAL* 3.6 8.0 - - + -
3D LYS* 2.9 25.3 + - - +
24D VAL* 3.4 21.1 - - + -
42D PHE* 3.9 21.8 - + + -
45D LEU* 3.7 17.0 - - + -
46D SER* 3.4 49.6 - - - -
49D TYR* 3.5 24.5 - - + -
52D VAL* 3.4 33.7 - - + -
53D ILE* 1.3 77.1 - - - +
55D LEU* 1.3 68.1 + - - +
101D ILE* 4.0 12.8 - - + -
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Residues in contact with LEU 55 (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 VAL* 3.6 2.9 - - - -
3D LYS* 3.2 25.8 - - + +
5D ILE* 4.2 17.7 - - + -
11D PHE* 4.3 15.5 - - + -
14D ALA* 3.6 31.6 - - + -
15D LEU* 4.6 2.0 - - + -
23D VAL* 3.6 28.0 - - + -
24D VAL 2.7 9.4 + - - +
25D VAL* 3.3 11.8 - - + -
26D ASP 3.0 21.8 + - - -
42D PHE* 3.3 9.4 - - - -
53D ILE* 3.8 15.9 - - + -
54D PHE* 1.3 87.1 - - - +
56D GLU* 1.3 61.9 + - - +
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Residues in contact with GLU 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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2D VAL* 3.8 15.3 - - + +
3D LYS 2.8 9.4 + - - +
4D GLN* 3.0 41.5 + - - +
5D ILE* 2.7 32.2 + - - +
26D ASP* 3.3 25.2 - - + +
28D SER* 4.0 15.2 - - - -
39D LYS* 3.4 37.4 + - - +
42D PHE* 5.4 0.7 - - + -
55D LEU* 1.3 74.1 - - - +
57D VAL* 1.3 68.2 + - - +
58D ASP* 4.3 6.8 + - - +
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Residues in contact with VAL 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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4D GLN* 4.4 0.4 - - - +
5D ILE* 3.9 22.2 - - + -
11D PHE* 4.6 2.9 - - + -
25D VAL* 3.8 19.5 - - + -
26D ASP 3.1 8.3 + - - -
27D PHE* 3.5 30.9 - - + -
28D SER 2.9 27.7 + - - +
56D GLU* 1.3 84.8 - - - +
58D ASP* 1.3 74.4 + - - +
59D VAL* 3.3 1.4 + - - +
62D CYS* 4.2 16.2 - - + +
65D VAL* 4.2 19.3 - - + -
66D ALA 5.0 0.4 - - - +
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Residues in contact with ASP 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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4D GLN* 3.9 15.1 - - - +
5D ILE 4.9 2.2 + - - -
28D SER* 3.3 7.0 - - - -
29D ALA* 3.9 4.4 + - - -
30D THR* 3.3 36.2 + - - +
56D GLU* 4.8 4.4 - - - +
57D VAL* 1.3 72.6 - - - +
59D VAL* 1.3 57.5 + - - +
60D ASP* 2.8 33.4 + - - +
61D ASP* 3.0 34.9 + - + +
62D CYS* 2.8 37.7 + - - +
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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