Contacts of the strand formed by residues 53 - 61 (chain A) 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 LEU 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A TYR* 4.0 14.1 - - + -
49A ASP* 3.0 9.9 - - - +
50A ARG 2.8 36.4 + - - +
51A ASN 3.1 3.5 - - - +
52A GLY* 1.3 81.7 - - - +
54A ASN* 1.3 61.8 + - - +
55A VAL* 4.7 14.1 - - + -
113A GLU* 4.3 11.9 - - + +
145A LYS 5.5 0.2 - - - +
146A VAL* 3.6 42.4 - - + +
149A LYS* 4.0 21.5 - - + -
151A LEU* 3.9 31.2 - - + -
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 5.9 2.9 - - - +
48A TYR 3.4 1.9 - - - +
49A ASP* 3.4 30.6 - - - +
52A GLY 4.0 2.0 + - - +
53A LEU* 1.3 77.9 - - - +
55A VAL* 1.3 68.0 + - - +
113A GLU* 3.7 24.4 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 3.5 6.1 - - - +
48A TYR* 2.8 42.3 + - + +
53A LEU* 4.7 15.0 - - + -
54A ASN* 1.3 82.2 + - - +
56A SER* 1.3 70.5 + - - +
57A ILE* 3.7 13.9 - - + -
111A ALA* 3.6 15.3 - - + -
112A TRP 3.3 17.7 - - - +
113A GLU* 4.0 6.5 - - + +
119A VAL* 3.8 28.0 - - + -
151A LEU* 4.4 6.1 - - + -
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS 3.2 10.1 - - - -
47A LYS* 4.6 3.4 - - - +
55A VAL* 1.3 74.8 - - - +
57A ILE* 1.3 62.4 + - - +
110A ILE 3.6 0.7 - - - +
111A ALA* 3.3 4.0 - - - -
112A TRP* 2.8 52.5 + - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.5 13.8 - - + +
45A PHE 3.6 12.8 - - - +
46A LYS* 2.8 32.7 + - - +
47A LYS 4.5 0.2 - - - -
48A TYR* 4.0 15.9 - - + +
55A VAL* 3.7 11.4 - - + -
56A SER* 1.3 82.0 - - - +
58A GLU* 1.3 63.4 + - - +
109A LEU* 4.1 25.8 - - + -
110A ILE 3.2 9.9 - - - +
111A ALA* 4.3 6.1 - - + -
151A LEU* 4.6 1.8 - - + -
154A PHE* 3.6 37.0 - - + -
155A LEU* 4.3 15.3 - - + -
158A ILE* 4.3 5.4 - - + -
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.4 4.3 - - - -
46A LYS* 5.7 2.7 - - - +
57A ILE* 1.3 76.6 - - - +
59A CYS* 1.3 62.5 + - - +
60A LYS* 3.9 30.9 + - + +
65A LEU* 4.1 16.3 - - - +
108A TYR 3.6 0.9 - - - +
109A LEU* 3.3 4.2 - - - -
110A ILE* 2.9 34.7 + - + +
112A TRP* 3.0 43.0 + - + +
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Residues in contact with CYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY 4.9 1.4 - - - +
37A ASP* 3.4 31.5 + - - +
38A PRO* 3.7 22.7 - - - -
39A LEU* 3.7 12.5 - - + +
46A LYS* 5.8 0.4 - - - +
58A GLU* 1.3 74.3 - - - +
60A LYS* 1.3 68.3 + - - +
107A TRP* 3.7 17.4 - - - -
108A TYR 3.2 9.0 - - - -
109A LEU* 3.7 12.6 - - + -
124A PHE* 3.9 17.9 - - - -
162A MET* 3.9 8.3 - - - -
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLU* 3.9 34.8 + - + +
59A CYS* 1.3 82.4 - - - +
61A ARG* 1.3 68.4 - - - +
64A GLY* 3.6 25.3 + - - +
65A LEU* 4.2 13.5 - - + -
107A TRP* 3.7 7.4 - - - -
108A TYR* 2.7 41.5 + - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN 2.9 27.1 + - - -
34A ARG* 3.3 12.3 + - - +
35A LEU 2.7 30.1 + - - -
36A GLY* 3.5 12.5 + - - -
60A LYS* 1.3 79.7 - - - +
62A VAL* 1.3 61.2 + - - +
63A SER* 3.7 20.2 - - - +
64A GLY* 2.8 22.1 + - - +
65A LEU* 3.9 2.3 + - - +
104A ASP 5.1 8.7 - - - +
106A ALA 3.6 8.5 - - - +
107A TRP* 3.5 28.2 - - + +
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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