Contacts of the strand formed by residues 75 - 81 (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 LYS 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU* 5.0 3.6 + - - -
48A SER* 3.0 10.6 + - - -
49A TYR* 3.1 49.4 + - + -
50A VAL* 3.0 26.3 + - - +
69A LEU* 4.8 3.4 - - - -
74A LEU* 1.3 79.4 - - - +
76A ALA* 1.3 62.8 + - - +
118A LEU 5.8 1.8 - - - +
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Residues in contact with ALA 76 (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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49A TYR* 4.4 2.5 - - - -
50A VAL 3.3 6.3 - - - -
52A LEU* 3.4 26.2 - - + -
69A LEU* 4.5 6.5 - - + +
75A LYS* 1.3 76.1 - - - +
77A ILE* 1.3 58.9 + - - +
78A GLY 4.4 2.9 - - - +
79A ILE* 4.5 0.9 - - + -
118A LEU* 4.0 34.2 + - + +
119A GLY 4.2 3.3 - - - +
120A ALA* 3.3 25.8 + - + -
121A ASN* 5.0 1.2 + - - -
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Residues in contact with ILE 77 (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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49A TYR* 3.9 17.3 - - + -
50A VAL 2.9 26.3 + - - +
51A ASP* 3.9 4.3 - - + +
75A LYS 3.5 2.2 + - - -
76A ALA* 1.3 74.5 - - - +
78A GLY* 1.3 59.5 + - - +
120A ALA* 3.8 0.7 - - - -
121A ASN* 2.8 44.0 + - - +
122A TYR* 3.5 21.4 + - + +
266A VAL* 3.6 36.1 - - + +
268A GLN* 3.8 24.7 - - + +
341A EDO 3.4 25.8 - - - +
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Residues in contact with GLY 78 (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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50A VAL 4.0 1.7 - - - +
51A ASP* 3.3 10.4 - - - -
52A LEU* 3.0 22.5 + - - +
76A ALA* 3.5 0.8 - - - +
77A ILE* 1.3 83.2 + - - +
79A ILE* 1.3 70.0 + - - +
120A ALA* 4.2 2.0 - - - -
122A TYR* 3.2 27.8 - - - -
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Residues in contact with ILE 79 (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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52A LEU* 3.3 21.5 - - + +
54A TYR* 3.6 27.6 - - + -
56A PHE* 5.2 2.0 - - + -
76A ALA* 4.5 2.2 - - + -
78A GLY* 1.3 82.9 - - - +
80A THR* 1.3 59.9 + - - +
81A PRO* 3.4 5.7 - - - +
111A SER* 4.0 19.7 - - - +
114A ILE* 3.7 26.7 - - + -
115A VAL* 3.6 28.7 - - + +
118A LEU* 3.9 17.3 - - + -
120A ALA* 4.4 3.4 - - + -
122A TYR 3.1 5.5 + - - -
123A VAL* 3.5 2.9 - - - -
124A LYS 2.8 25.7 + - - +
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Residues in contact with THR 80 (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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14A TRP* 4.0 3.4 - - - -
51A ASP* 2.6 24.8 + - - -
52A LEU 2.9 9.3 + - - -
53A PRO* 3.2 10.4 - - - +
54A TYR 2.9 22.4 + - - -
79A ILE* 1.3 71.5 - - - +
81A PRO* 1.4 71.0 - - - +
82A GLU* 3.3 1.7 + - - +
84A TYR* 4.0 9.9 - - + +
124A LYS* 2.9 42.7 + - - +
126A TRP* 5.3 2.5 - - + +
337A UNL 3.7 21.8 - - - +
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Residues in contact with PRO 81 (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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54A TYR 3.3 8.7 - - - +
79A ILE* 3.4 11.9 - - - +
80A THR* 1.4 85.8 - - - +
82A GLU* 1.3 60.0 + - - +
83A ILE* 2.9 23.6 + - + +
84A TYR* 3.7 7.3 - - - -
107A LEU* 4.2 9.0 - - + -
108A MSE 3.8 29.8 - - + -
111A SER* 3.5 26.7 - - - +
123A VAL* 3.6 14.4 - - + -
124A LYS 3.4 12.9 - - - +
125A VAL* 5.3 2.0 - - - -
126A TRP 5.6 1.0 + - - -
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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