Contacts of the strand formed by residues 44 - 48 (chain D) in PDB entry 4LOU
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 LYS 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D TYR* 3.1 5.4 - - - -
36D GLN* 2.7 47.5 + - - +
41D THR* 3.3 30.8 - - + +
42D SER* 3.5 14.9 + - - +
43D PRO* 1.3 76.9 - - - +
45D ARG* 1.3 66.4 + - - +
46D TRP* 4.0 21.1 - - + +
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Residues in contact with ARG 45 (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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107C TYR* 3.4 46.0 + - - -
108C PHE 3.9 5.2 - - - -
109C ASP* 2.8 42.7 + - - +
110C VAL* 5.6 0.4 - - - +
111C TRP* 4.7 2.8 - - - +
33D HIS* 5.4 1.3 - - + -
34D TRP 4.6 1.6 - - - +
35D TYR* 3.4 24.1 - - + -
43D PRO 4.2 0.4 + - - -
44D LYS* 1.3 71.7 - - - +
46D TRP* 1.3 68.9 + - - +
47D ILE 4.8 3.4 - - - +
48D TYR* 3.2 30.0 - - + -
54D THR* 3.1 53.1 + - + +
57D VAL* 4.3 0.3 - - - +
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Residues in contact with TRP 46 (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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34D TRP* 2.6 25.1 + - + +
35D TYR 4.5 0.2 - - - -
36D GLN* 3.5 51.1 - - + +
44D LYS* 3.2 20.6 + - + +
45D ARG* 1.3 83.4 - - - +
47D ILE* 1.3 73.9 + - + +
54D THR* 3.4 13.1 + - - -
56D GLY 5.6 0.9 - - - -
57D VAL* 3.2 53.5 - - + +
58D PRO* 4.3 7.9 - - + -
61D PHE* 3.3 50.8 - + - -
72D LEU* 4.6 2.7 - - + -
85D TYR* 4.2 11.7 - + + -
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Residues in contact with ILE 47 (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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33D HIS* 3.1 4.5 - - - +
34D TRP* 2.6 52.1 + - + +
45D ARG* 5.0 1.3 - - - +
46D TRP* 1.3 91.3 - - + +
48D TYR* 1.3 62.2 + - - +
50D THR 4.0 24.0 - - - +
51D SER 4.3 2.0 - - - -
52D LYS 3.2 12.3 - - - +
53D LEU* 3.6 16.6 - - + -
61D PHE* 4.4 6.3 - - + -
62D SER 3.8 37.5 - - - +
63D GLY* 4.6 1.6 - - - -
72D LEU* 4.1 21.8 - - + -
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Residues in contact with TYR 48 (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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234B HIS* 5.8 0.8 - + - -
235B GLU* 5.1 8.0 + - - -
102C GLY* 4.7 6.5 - - - -
107C TYR* 3.9 22.9 - + + -
33D HIS* 3.4 18.2 - - + +
45D ARG* 3.2 30.1 - - - +
47D ILE* 1.3 74.2 - - - +
49D ASP* 1.3 97.5 + - - +
50D THR 3.5 1.6 - - - -
51D SER 4.4 0.2 - - - -
52D LYS* 2.8 65.9 + - + +
53D LEU 3.3 24.0 + - - -
54D THR* 3.7 7.2 - - - -
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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