Contacts of the strand formed by residues 62 - 68 (chain D) in PDB entry 1KTD
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 GLU 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LYS* 3.1 33.0 + - - +
140A ARG* 5.2 3.5 + - - -
82C ASP* 4.9 7.4 - - - +
24D GLY* 4.9 5.2 - - - +
58D PHE* 3.2 4.6 - - - -
59D TYR* 3.0 32.2 + - - +
60D ASN 3.6 0.4 - - - -
61D LEU* 1.3 83.9 - - + +
63D GLU* 1.3 66.9 + - - +
64D ASN* 3.2 4.5 + - + +
78D THR* 3.8 25.2 + - + +
80D LEU* 5.9 2.8 - - - +
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Residues in contact with GLU 63 (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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56D ARG* 2.8 45.1 + - + +
57D TYR 3.3 11.2 - - - +
58D PHE* 3.5 23.3 - - + -
61D LEU 4.2 0.6 + - - -
62D GLU* 1.3 72.2 - - - +
64D ASN* 1.3 58.5 + - - +
65D LEU 4.5 5.4 - - - +
66D ARG* 2.7 39.7 + - - +
77D VAL* 3.3 27.6 - - + +
78D THR* 3.7 10.0 - - - +
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C MET* 4.0 13.7 - - - +
36D GLU* 5.6 1.0 + - - -
57D TYR* 2.9 17.4 + - - +
58D PHE 3.9 1.2 - - - -
59D TYR* 3.3 41.5 - - + +
62D GLU* 3.2 4.6 + - + +
63D GLU* 1.3 73.7 - - - +
65D LEU* 1.3 72.3 + - - +
77D VAL* 2.7 27.1 + - - -
78D THR* 3.1 23.7 + - - +
80D LEU* 4.0 8.3 - - + +
81D GLY* 3.4 24.5 - - - +
84D ASP* 4.7 2.3 - - - +
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Residues in contact with LEU 65 (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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56D ARG* 3.8 0.2 - - - -
57D TYR* 2.9 46.2 + - + +
63D GLU* 4.5 2.1 - - - +
64D ASN* 1.3 92.1 + - - +
66D ARG* 1.3 67.8 + - - +
74D PHE* 4.2 4.9 - - + -
75D ARG 3.5 28.3 - - - +
76D ALA* 3.8 2.7 - - - +
77D VAL* 3.6 9.2 - - - +
81D GLY* 3.5 21.8 - - - +
84D ASP* 3.9 15.3 - - + +
85D ALA* 3.9 12.8 - - + +
88D TRP* 3.5 35.0 - - + -
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Residues in contact with ARG 66 (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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800B SO4 3.4 36.8 + - - -
52D ARG* 4.3 2.4 - - - +
54D LEU* 3.9 22.6 - - + +
55D VAL* 3.1 16.6 - - - +
56D ARG* 3.7 17.2 - - - +
57D TYR* 4.7 2.2 - - - -
63D GLU* 2.7 29.7 + - - +
65D LEU* 1.3 77.8 - - - +
67D PHE* 1.3 61.8 + - - +
68D ASP* 4.1 8.7 + - + +
73D GLU 4.3 0.2 - - - +
74D PHE* 3.4 9.3 - - - +
75D ARG* 3.0 39.2 + - + +
77D VAL* 3.6 18.2 - - + +
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Residues in contact with PHE 67 (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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53D LEU* 3.5 14.7 - - + +
54D LEU* 3.3 5.7 + - - -
55D VAL* 2.9 47.0 + - + +
66D ARG* 1.3 74.6 - - - +
68D ASP* 1.3 59.5 + - - +
69D SER* 4.0 20.9 - - - -
72D GLY* 3.6 29.8 - - - -
73D GLU* 3.7 13.7 - - - -
74D PHE* 3.5 45.3 - + + -
95D LEU* 4.4 4.9 - - + -
98D LYS* 3.8 31.2 - - + -
99D ARG* 3.9 17.9 - - + -
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Residues in contact with ASP 68 (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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45B TYR* 4.3 6.9 + - - -
52B ARG* 4.7 0.3 + - - -
52D ARG* 2.9 43.4 + - - +
53D LEU 3.6 4.4 - - - +
54D LEU* 4.1 10.5 - - + -
66D ARG* 4.1 9.9 + - + -
67D PHE* 1.3 76.4 - - - +
69D SER* 1.3 59.0 + - - +
70D ASP* 2.9 33.9 + - - +
71D VAL* 2.6 41.0 + - + +
72D GLY 3.0 9.4 + - - -
73D GLU 4.2 4.7 + - - +
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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