Contacts of the strand formed by residues 53 - 58 (chain E) in PDB entry 1XSK
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 PHE 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E ILE* 3.3 42.6 - - + -
18E HIS 3.5 22.7 - - - -
19E PRO* 3.5 33.2 - - + -
34E VAL 3.7 0.5 - - - +
35E TYR* 3.4 0.9 - - - -
36E ALA* 2.8 41.6 + - - +
38E PRO* 4.3 10.3 - - + -
51E PRO* 5.4 0.7 - - + -
52E LEU* 1.3 77.4 - - - +
54E THR* 1.3 58.1 + - - +
55E LEU* 4.1 8.5 - - + -
69E ILE* 4.3 10.1 - - + -
70E GLU 3.7 17.5 - - - -
71E HIS* 4.3 13.0 - + + +
138E GLY* 4.1 4.3 - - - -
139E TYR* 3.7 18.4 - - + -
150E MET* 4.0 14.8 - - + -
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Residues in contact with THR 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D GLN* 5.5 2.4 + - - -
353D LYS* 6.1 0.2 - - - -
33E VAL* 3.9 25.6 - - + -
34E VAL 3.6 2.5 - - - -
35E TYR* 3.8 21.0 - - + -
52E LEU* 3.8 7.1 + - - +
53E PHE* 1.3 75.0 - - - +
55E LEU* 1.3 63.8 + - - +
56E ARG* 5.1 8.5 - - + +
68E ARG 3.2 4.7 - - - +
69E ILE* 3.5 0.2 - - - -
70E GLU* 3.0 56.4 + - - +
71E HIS 5.7 0.7 + - - -
73E GLN* 4.2 12.6 + - - +
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 4.5 3.6 - - + -
32E MET 3.6 2.1 - - - +
33E VAL* 3.5 1.7 - - - -
34E VAL* 2.7 51.3 + - + +
36E ALA* 4.4 12.6 - - + -
53E PHE* 4.1 22.4 - - + +
54E THR* 1.3 78.3 - - - +
56E ARG* 1.3 60.4 + - - +
57E PHE* 3.9 28.2 - - + -
67E VAL* 5.0 1.3 - - + -
68E ARG 3.4 4.0 - - - +
69E ILE* 4.0 32.8 - - + -
112E VAL* 5.4 0.2 - - + -
118E TRP* 3.9 27.8 - - + -
120E LEU* 4.8 8.7 - - + -
137E ASN* 5.0 2.2 - - - +
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Residues in contact with ARG 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLN* 2.9 31.9 + - - +
31E GLU* 2.9 36.5 + - + +
32E MET 3.5 3.1 - - - +
33E VAL* 3.3 28.4 - - + +
35E TYR* 5.8 0.4 + - - -
54E THR* 4.0 8.0 + - + +
55E LEU* 1.3 74.5 - - - +
57E PHE* 1.3 68.6 + - - +
58E PHE* 4.0 10.0 - - + -
66E GLY 3.5 1.0 - - - +
67E VAL* 3.4 6.6 - - - +
68E ARG* 2.9 52.5 + - + +
70E GLU* 5.3 8.9 + - - +
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Residues in contact with PHE 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLU* 3.5 6.2 - - - +
32E MET* 2.8 52.6 + - + +
34E VAL* 4.1 11.9 - - + -
55E LEU* 3.9 30.3 - - + -
56E ARG* 1.3 73.8 - - - +
58E PHE* 1.3 61.3 + - - +
65E VAL* 4.3 1.1 - - + -
66E GLY 3.3 4.0 - - - +
67E VAL* 3.8 37.5 - - + -
103E PHE* 3.6 28.2 - - + -
110E ALA* 3.6 29.8 - - + -
112E VAL* 3.8 30.3 - - + -
120E LEU* 4.3 9.9 - - + -
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Residues in contact with PHE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ASN* 6.2 0.2 - - - +
31E GLU* 3.5 30.1 - - + +
56E ARG* 4.0 16.8 - - + -
57E PHE* 1.3 76.8 - - - +
59E SER* 1.3 61.2 + - - +
60E PRO* 4.6 10.1 - - + -
65E VAL* 3.6 3.8 - - - -
66E GLY* 2.6 55.2 + - - -
67E VAL 3.9 2.7 - - - -
68E ARG* 4.3 7.9 - - + -
86E ILE* 5.5 11.4 - - + -
103E PHE* 3.5 10.7 - - - -
238E GLU* 3.5 26.9 - - - -
240E PHE* 3.7 32.5 - + - -
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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