Contacts of the strand formed by residues 55 - 61 (chain D) in PDB entry 4U9W
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 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D LYS* 3.4 7.9 - - - +
48D TYR* 2.8 38.0 + - + +
53D LEU* 4.8 14.4 - - + -
54D ASN* 1.3 81.2 + - - +
56D SER* 1.3 60.3 + - - +
57D ILE* 3.8 16.6 - - + -
111D ALA* 3.5 24.0 - - + -
112D TRP 3.4 16.2 - - - +
113D GLU* 4.0 6.7 - - + +
119D VAL* 3.7 28.0 - - + -
151D LEU* 4.2 12.1 - - + -
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Residues in contact with SER 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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46D LYS 3.2 9.2 - - - -
47D LYS* 4.5 1.1 - - - +
55D VAL* 1.3 72.2 - - - +
57D ILE* 1.3 63.4 + - - +
110D ILE 3.3 1.6 - - - +
111D ALA* 3.2 4.3 - - - -
112D TRP* 2.8 54.2 + - - +
115D SER* 5.5 3.8 - - - -
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Residues in contact with ILE 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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39D LEU* 4.5 4.8 - - + +
45D PHE 3.9 8.7 - - - +
46D LYS* 2.6 40.3 + - - +
47D LYS 4.6 0.2 - - - -
48D TYR* 4.0 19.3 - - + +
55D VAL* 3.8 11.4 - - + -
56D SER* 1.3 81.6 - - - +
58D GLU* 1.3 65.0 + - - +
109D LEU* 4.1 25.8 - - + -
110D ILE 3.2 8.3 - - - +
111D ALA* 4.2 7.9 - - + -
151D LEU* 4.3 7.6 - - + -
154D PHE* 3.8 34.8 - - + -
155D LEU* 4.2 7.6 - - + -
158D ILE* 4.1 12.6 - - + -
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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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39D LEU* 4.7 2.2 - - - -
46D LYS* 5.3 5.2 - - + +
57D ILE* 1.3 77.0 - - - +
59D CYS* 1.3 60.0 + - - +
60D LYS* 3.3 43.3 + - + +
65D LEU* 4.1 5.4 - - - +
108D TYR 3.5 1.0 - - - +
109D LEU* 3.2 6.9 - - - +
110D ILE* 2.9 42.2 + - + +
112D TRP* 3.1 42.1 + - + +
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Residues in contact with CYS 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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36D GLY 4.8 1.4 - - - +
37D ASP* 3.5 19.9 + - - +
38D PRO* 3.9 10.8 - - - +
39D LEU* 4.0 23.7 - - + +
46D LYS* 5.5 0.8 - - - +
58D GLU* 1.3 72.6 - - - +
60D LYS* 1.3 66.7 + - - +
107D TRP* 3.9 19.0 - - - -
108D TYR 3.2 4.0 - - - -
109D LEU* 3.7 13.9 - - + -
124D PHE* 3.7 31.9 - - - -
162D MET* 3.9 12.3 - - - -
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Residues in contact with LYS 60 (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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36D GLY 5.7 0.9 - - - -
58D GLU* 3.3 40.1 + - + +
59D CYS* 1.3 80.3 - - - +
61D ARG* 1.3 67.0 + - - +
64D GLY* 3.7 23.6 + - - +
65D LEU* 4.3 13.2 - - + -
107D TRP* 3.5 8.7 - - - -
108D TYR* 2.7 40.9 + - - +
110D ILE* 6.1 0.2 - - + -
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Residues in contact with ARG 61 (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 ASN 3.0 26.7 + - - -
34D ARG* 3.3 12.5 + - - +
35D LEU 2.4 30.8 + - - -
36D GLY* 3.7 12.9 + - - -
60D LYS* 1.3 76.1 - - - +
62D VAL* 1.3 61.2 + - - +
63D SER* 3.1 20.4 - - - +
64D GLY* 2.8 23.4 + - - +
65D LEU* 3.6 6.6 + - - +
104D ASP 5.3 8.5 - - - +
106D ALA 3.6 9.6 - - - +
107D TRP* 3.4 29.2 - - + +
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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