Contacts of the strand formed by residues 51 - 59 (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 VAL 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D HIS 3.5 8.3 - - - +
44D PHE* 3.7 26.5 - - + -
45D TYR* 4.6 2.4 - - - -
48D THR* 3.8 9.2 - - - +
49D GLN 4.2 0.4 - - - -
50D ARG* 1.3 81.0 - - - +
52D ARG* 1.3 67.5 + - - +
53D LEU 4.3 0.5 + - - -
69D SER* 4.4 3.3 + - - -
102D VAL* 4.3 19.1 - - + +
106D CYS* 3.8 34.1 - - + -
107D ARG* 3.7 34.4 + - - +
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Residues in contact with ARG 52 (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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52B ARG* 3.4 21.6 - - - +
68B ASP* 4.7 0.8 + - - -
70B ASP* 4.7 0.2 - - - -
800B SO4 2.7 43.9 + - - -
41D GLU 3.5 1.6 - - - +
42D CYS* 3.6 0.5 - - - -
43D HIS* 2.7 56.3 + - + +
45D TYR* 3.2 36.3 + - + +
51D VAL* 1.3 76.5 - - - +
53D LEU* 1.3 62.9 + - - +
54D LEU* 4.0 17.6 - - - +
66D ARG* 4.3 2.0 - - - +
68D ASP* 2.9 38.1 + - - +
69D SER* 3.5 11.9 - - - +
70D ASP* 3.2 19.4 + - - +
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.6 32.8 - - + -
40D SER 4.7 0.2 - - - -
41D GLU 3.1 28.3 - - - +
42D CYS* 4.3 1.8 - - - +
51D VAL 4.2 0.4 + - - -
52D ARG* 1.3 73.6 - - - +
54D LEU* 1.3 65.2 + - - +
55D VAL* 4.3 12.1 - - + -
67D PHE* 3.5 15.2 - - + +
68D ASP* 3.6 2.9 - - - +
69D SER* 2.9 35.6 + - - +
98D LYS* 4.0 22.0 - - - +
101D GLU* 4.3 9.2 - - + +
102D VAL* 4.0 21.7 - - + +
106D CYS* 4.0 16.8 - - - -
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Residues in contact with LEU 54 (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 3.9 21.5 - - - +
39D LYS 3.5 3.1 - - - +
41D GLU* 2.6 51.3 + - + +
43D HIS* 4.3 14.8 - - + +
52D ARG* 4.0 12.5 + - - +
53D LEU* 1.3 75.6 - - - +
55D VAL* 1.3 68.5 + - - +
56D ARG* 3.7 24.5 - - + +
66D ARG* 3.9 39.3 - - - +
67D PHE 3.3 8.5 - - - +
68D ASP* 4.1 12.6 - - + -
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Residues in contact with VAL 55 (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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8D LEU* 4.2 13.0 - - + -
38D CYS* 3.6 17.9 - - - -
39D LYS 3.2 3.1 - - - -
40D SER* 3.8 20.6 - - - +
53D LEU* 4.3 11.0 - - + -
54D LEU* 1.3 73.6 - - - +
56D ARG* 1.3 66.9 + - - +
57D TYR* 3.5 31.6 - - + +
66D ARG* 3.1 10.7 - - - +
67D PHE* 2.9 48.4 + - + +
74D PHE* 5.6 0.9 - - + -
98D LYS* 4.8 11.2 - - - +
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Residues in contact with ARG 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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800B SO4 5.4 3.2 + - - -
141C ASP* 3.2 28.8 + - - +
142C ASP* 4.4 3.8 - - - +
38D CYS* 3.2 4.5 - - - -
39D LYS* 2.7 45.0 + - + +
41D GLU* 2.8 33.6 + - - +
54D LEU* 3.7 26.3 - - + +
55D VAL* 1.3 80.6 - - - +
57D TYR* 1.3 61.5 + - - +
58D PHE* 3.3 32.1 - - + -
63D GLU* 2.8 38.5 + - - +
65D LEU 3.8 3.6 - - - -
66D ARG* 3.7 7.0 - - - +
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Residues in contact with TYR 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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69C ASN* 5.5 2.2 - - - -
9D LYS 5.5 0.2 + - - -
10D GLN* 2.7 34.0 + - - -
11D ALA* 4.6 2.9 + - - +
36D GLU* 3.8 21.8 - - - +
37D TYR 3.5 1.1 - - - -
38D CYS* 3.6 18.8 - - + -
55D VAL* 3.5 23.2 - - + +
56D ARG* 1.3 74.1 - - - +
58D PHE* 1.3 62.0 + - - +
63D GLU* 3.3 5.6 - - - +
64D ASN* 2.9 40.9 + - - +
65D LEU* 2.9 37.4 + - + +
66D ARG* 4.6 1.3 - - - -
74D PHE* 4.5 10.6 - + - -
88D TRP* 3.8 34.4 - + - -
98D LYS* 5.5 5.0 + - - -
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Residues in contact with PHE 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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142C ASP 4.1 0.4 - - - -
143C HIS* 3.5 33.9 - - + -
35D LEU 3.4 2.4 - - - +
36D GLU* 3.9 4.5 + - - +
37D TYR* 2.6 66.9 + + + +
39D LYS* 3.5 37.0 - - + -
56D ARG* 3.3 33.4 - - + -
57D TYR* 1.3 75.6 - - - +
59D TYR* 1.3 61.1 + - - +
60D ASN 3.8 10.7 + - - +
62D GLU 3.2 7.4 - - - +
63D GLU* 3.5 42.6 - - + -
64D ASN* 3.9 1.3 - - - -
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Residues in contact with TYR 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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70C LEU* 4.0 19.3 - - + -
73C MET* 3.5 40.2 - - + -
74C LYS* 3.9 6.0 - - - -
77C SER* 3.2 33.8 + - - -
80C THR 3.9 5.3 + - - -
82C ASP* 4.4 1.4 - - - +
34D PHE* 3.3 21.7 - - + -
35D LEU 3.3 10.5 - - - -
36D GLU* 4.5 3.6 - - - +
58D PHE* 1.3 71.9 - - - +
60D ASN* 1.3 100.1 + - - +
61D LEU 3.1 2.8 + - - -
62D GLU* 3.0 18.1 + - - +
64D ASN* 3.3 18.4 - - + +
80D LEU* 4.5 18.2 - - + -
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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