Contacts of the strand formed by residues 47 - 56 (chain A) in PDB entry 1XTD
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 ARG 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL 3.4 0.5 - - - +
43A CYS* 3.1 5.5 - - - -
44A ILE 2.7 36.6 + - - +
45A ASN* 3.8 13.0 - - + +
46A GLY* 1.3 79.2 - - - -
48A PRO* 1.3 72.4 - - - +
49A CYS* 3.5 2.8 - - - -
73A ASP* 2.7 47.6 + - - +
75A PHE* 3.7 18.1 - - - +
76A THR* 3.3 21.4 - - - +
80A LEU* 4.3 13.0 - - + -
160A MSE 4.0 2.7 - - - -
162A THR* 4.5 14.8 + - - +
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Residues in contact with PRO 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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41A TYR* 5.4 0.9 - - + -
42A VAL 3.7 4.3 - - - +
46A GLY 4.4 1.3 - - - +
47A ARG* 1.3 100.8 - - + +
49A CYS* 1.3 60.2 + - - +
73A ASP* 3.7 4.2 - - - +
74A ILE* 3.2 28.6 + - + +
75A PHE* 3.8 28.7 - - + -
93A PRO* 3.9 16.6 - - + -
95A VAL* 5.7 0.2 - - + -
159A ALA* 4.1 11.2 - - + -
160A MSE 3.7 30.3 - - + -
162A THR* 6.0 0.4 - - - +
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Residues in contact with CYS 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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41A TYR* 3.0 14.7 - - - -
42A VAL* 2.9 37.4 + - + +
44A ILE* 4.4 9.4 - - - -
47A ARG* 3.5 15.9 - - - -
48A PRO* 1.3 79.4 - - - +
50A LYS* 1.3 59.3 + - - +
51A VAL 4.1 0.2 - - - -
71A ALA* 3.5 23.3 - - + -
72A THR 3.3 7.6 - - - +
73A ASP* 4.0 11.0 - - - -
74A ILE* 4.2 1.3 - - - +
80A LEU* 3.9 28.7 - - - -
93A PRO* 4.7 0.6 - - - +
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Residues in contact with LYS 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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39A GLY* 3.4 36.9 + - - +
40A GLY 3.2 4.0 - - - +
41A TYR* 4.3 21.9 + - + -
49A CYS* 1.3 72.7 - - - +
51A VAL* 1.3 66.6 + - - +
52A ILE* 3.3 10.4 + - + +
71A ALA* 3.6 2.2 - - - -
72A THR* 2.8 34.8 + - - +
74A ILE* 3.9 16.0 - - + +
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Residues in contact with VAL 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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36A LEU* 4.9 11.4 - - + -
37A LYS 3.7 14.4 - - - +
38A LYS* 3.8 15.7 - - - +
39A GLY* 2.9 27.0 + - - -
40A GLY 2.6 22.1 + - - +
42A VAL* 3.8 27.4 - - + -
50A LYS* 1.3 71.4 - - - +
52A ILE* 1.3 62.7 + - - +
53A ASP 3.6 23.3 - - - +
54A LEU* 4.1 14.1 - - + -
69A ILE* 4.1 10.5 - - + -
70A VAL 3.9 1.6 - - - +
71A ALA* 3.7 5.2 - - - -
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Residues in contact with ILE 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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38A LYS* 3.4 29.8 + - - +
50A LYS* 3.3 15.4 + - + +
51A VAL* 1.3 76.3 - - - +
53A ASP* 1.3 79.9 + - - +
70A VAL* 2.9 35.1 + - + +
71A ALA* 4.1 2.0 - - - -
72A THR* 3.7 29.2 - - - +
79A ARG* 5.0 9.4 - - + +
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Residues in contact with ASP 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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38A LYS* 4.4 11.6 + - - +
51A VAL* 3.6 8.2 - - - +
52A ILE* 1.3 99.5 - - - +
54A LEU* 1.3 61.6 + - - +
68A SER 4.5 0.7 - - - -
69A ILE* 3.7 0.7 - - - -
70A VAL* 2.8 52.6 + - + +
79A ARG* 5.0 4.3 + - - -
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Residues in contact with LEU 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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36A LEU* 4.0 29.6 - - + +
37A LYS* 5.4 0.2 - - - -
38A LYS* 4.5 20.5 - - + +
51A VAL* 4.1 18.2 - - + -
53A ASP* 1.3 75.9 - - - +
55A SER* 1.3 65.3 + - - +
56A VAL* 4.0 22.9 - - + -
67A VAL* 4.2 16.4 - - + -
68A SER 3.5 8.3 - - - +
69A ILE* 4.3 9.0 - - + -
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Residues in contact with SER 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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54A LEU* 1.3 77.8 - - - +
56A VAL* 1.3 72.0 + - - +
57A SER 4.2 0.2 - - - -
66A LYS 4.0 0.2 - - - +
67A VAL* 3.7 0.9 - - - +
68A SER* 2.7 55.1 + - - +
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Residues in contact with VAL 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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34A GLY* 6.4 0.2 - - - -
54A LEU* 4.0 21.5 - - + -
55A SER* 1.3 86.0 + - - +
57A SER* 1.3 74.8 + - - +
58A LYS* 4.0 5.3 + - - +
65A ALA* 4.6 9.9 - - + -
66A LYS 3.6 5.8 - - - +
67A VAL* 4.1 19.1 - - + -
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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