Contacts of the strand formed by residues 47 - 54 (chain A) in PDB entry 3KTC
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.7 3.4 - - + +
10A GLY* 3.7 32.5 - - - +
11A ALA* 4.0 10.5 - - + +
16A PHE* 3.9 33.4 - - + -
41A ALA* 3.9 23.5 + - + +
44A VAL* 4.2 13.0 - - + -
45A GLY 4.6 1.0 - - - +
46A GLU* 1.3 79.7 - - - +
48A SER* 1.3 62.1 + - - +
49A TYR 4.4 4.9 - - - +
50A VAL* 4.8 1.1 - - + -
72A ALA 5.1 1.7 - - - +
73A GLY 4.1 4.5 - - - +
74A LEU* 3.4 21.6 - - + +
269A LEU* 4.9 4.0 - - + -
282A ALA* 5.4 0.7 - - + -
286A ILE* 3.8 20.6 - - + -
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Residues in contact with SER 48 (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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8A GLU* 4.3 20.1 + - - +
9A PHE 2.8 9.9 + - - -
46A GLU 3.9 4.4 + - - -
47A LEU* 1.3 75.3 + - - +
49A TYR* 1.3 86.1 + - - +
73A GLY 3.9 6.6 - - - +
74A LEU* 3.5 10.1 - - - -
75A LYS* 3.0 25.4 + - - +
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Residues in contact with TYR 49 (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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8A GLU* 3.3 37.9 + - + -
9A PHE 3.3 2.2 + - - -
10A GLY* 3.0 27.2 - - - -
11A ALA 3.1 4.0 + - - -
47A LEU* 3.7 3.7 - - - +
48A SER* 1.3 89.5 - - - +
50A VAL* 1.3 69.0 + - - +
74A LEU* 3.9 2.2 - - - +
75A LYS* 3.1 62.6 + - + +
76A ALA 4.9 2.2 - - - -
77A ILE* 3.9 30.1 - - + -
121A ASN* 5.7 5.6 - - - -
266A VAL* 3.6 31.2 - - + -
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Residues in contact with VAL 50 (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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11A ALA* 3.1 15.9 - - + +
13A LEU* 4.2 21.8 - - + +
16A PHE* 5.2 0.2 - - + -
41A ALA* 4.1 15.9 - - + -
47A LEU* 4.8 3.4 - - + -
49A TYR* 1.3 81.0 - - - +
51A ASP* 1.3 57.9 + - - +
52A LEU* 3.8 15.9 - - + +
69A LEU* 3.7 31.2 - - + -
74A LEU* 4.0 21.1 - - + -
75A LYS 3.0 9.0 + - - +
76A ALA* 3.3 8.3 - - - -
77A ILE* 2.9 30.2 + - - -
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Residues in contact with ASP 51 (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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11A ALA 3.1 6.7 + - - -
12A GLY* 4.1 0.7 - - - -
13A LEU* 2.8 25.2 + - - +
14A TRP* 3.5 18.9 - - + -
50A VAL* 1.3 72.0 - - - +
52A LEU* 1.3 62.5 + - - +
77A ILE* 4.1 5.6 - - + -
78A GLY* 3.3 19.5 - - - +
80A THR* 2.6 35.3 + - - -
122A TYR* 4.3 5.6 + - - +
124A LYS* 3.2 25.6 + - - +
199A LEU* 5.8 0.2 - - - +
268A GLN* 3.7 17.4 + - - +
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Residues in contact with LEU 52 (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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13A LEU* 4.3 11.9 - - + -
34A THR* 4.5 1.8 - - + -
38A ILE* 4.2 15.9 - - + -
50A VAL* 3.8 22.0 - - + +
51A ASP* 1.3 75.7 - - - +
53A PRO* 1.3 71.1 - - + +
56A PHE* 4.2 10.8 - - + -
65A VAL* 3.6 31.9 - - + -
69A LEU* 4.4 7.6 - - + -
76A ALA* 3.4 33.0 - - + -
78A GLY 3.0 8.3 + - - +
79A ILE* 3.3 21.9 - - + +
80A THR 2.9 20.3 + - - -
118A LEU* 4.6 0.9 - - + -
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Residues in contact with PRO 53 (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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13A LEU* 4.0 18.6 - - + -
14A TRP* 3.7 26.2 - - + -
34A THR* 5.3 1.0 + - - +
37A GLN* 5.6 1.8 - - - +
51A ASP 3.6 8.3 - - - +
52A LEU* 1.3 86.2 - - + +
54A TYR* 1.3 57.9 + - - +
55A PRO 3.6 5.9 - - - +
56A PHE* 3.6 22.0 - - - -
80A THR* 3.2 10.5 - - - +
82A GLU* 3.8 26.9 - - + +
84A TYR* 4.7 0.9 - - - +
337A UNL 4.3 9.2 - - - +
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Residues in contact with TYR 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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53A PRO* 1.3 74.3 - - - +
55A PRO* 1.3 80.8 - - + +
56A PHE* 3.7 36.1 - + + -
79A ILE* 3.6 20.9 - - + -
80A THR 2.9 7.5 + - - +
81A PRO* 3.3 6.0 - - + +
82A GLU* 2.8 25.8 + - - -
107A LEU* 3.9 17.8 - - + +
110A GLU* 2.6 38.3 + - + +
111A SER* 4.3 8.7 - - - -
114A ILE* 3.7 39.7 - - + +
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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