Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 5X6E
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 THR 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.9 26.5 - - + -
20A LYS 4.1 2.9 - - - +
21A GLN* 2.6 34.0 + - + +
41A LEU* 3.4 6.2 - - - +
42A TYR* 3.1 33.5 + - + -
43A ASP* 3.1 23.3 + - - +
91A GLN 5.3 0.3 + - - -
92A ALA* 1.3 74.9 - - - +
94A ALA* 1.3 62.2 + - - +
95A TYR* 5.0 5.4 - - + -
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Residues in contact with ALA 94 (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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19A PRO* 3.5 2.6 - - - +
20A LYS* 2.8 36.4 + - - +
22A PHE* 4.0 22.9 - - + -
28A ILE* 4.5 8.1 - - + -
39A ILE* 4.3 15.5 - - + -
40A PHE 3.4 9.9 - - - +
41A LEU* 4.3 11.0 - - + -
92A ALA* 4.4 1.1 - - + -
93A THR* 1.3 76.8 - - - +
95A TYR* 1.3 66.2 + - - +
96A VAL* 3.9 2.5 + - + +
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 4.5 11.6 + - - -
12A LEU* 3.4 39.9 - - + -
13A GLU* 5.4 3.4 - - - -
17A ILE* 4.2 11.7 - - + -
18A LYS 4.1 6.7 - - - -
19A PRO* 3.4 50.1 - - + +
38A CYS 3.7 0.7 - - - +
39A ILE* 4.7 1.1 - - - -
40A PHE* 2.8 59.3 + + + +
42A TYR* 4.5 17.6 - + + -
93A THR* 5.0 3.4 - - + -
94A ALA* 1.3 75.9 - - - +
96A VAL* 1.3 65.1 + - - +
97A ILE* 3.3 9.7 + - + +
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Residues in contact with VAL 96 (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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17A ILE* 4.0 12.4 - - - +
18A LYS 5.4 1.8 + - - -
20A LYS* 5.2 7.7 - - + +
22A PHE* 3.5 34.8 - - + -
28A ILE* 4.3 12.3 - - + +
37A TYR* 3.7 39.3 - - + -
38A CYS 4.5 1.1 - - - -
39A ILE* 4.7 7.0 - - + -
94A ALA* 3.9 5.3 + - + +
95A TYR* 1.3 70.3 - - - +
97A ILE* 1.3 64.1 + - - +
98A LYS 5.1 0.2 - - - +
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Residues in contact with ILE 97 (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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8A PHE* 6.1 3.6 - - + -
12A LEU* 4.4 15.9 - - + -
17A ILE* 3.8 29.4 - - + -
37A TYR* 3.1 5.2 - - - +
38A CYS* 2.6 61.0 + - - +
40A PHE* 4.5 7.9 - - + +
95A TYR* 3.3 13.7 - - + +
96A VAL* 1.3 81.5 - - - +
98A LYS* 1.3 66.9 + - - +
101A GLU* 3.0 40.2 - - + +
102A LEU* 5.9 1.6 - - + -
105A LEU* 4.8 4.5 - - + -
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Residues in contact with LYS 98 (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 GLU 3.6 10.1 - - - +
37A TYR* 3.8 18.8 - - + -
38A CYS 4.1 1.6 + - - -
96A VAL* 6.2 0.2 - - + -
97A ILE* 1.3 83.3 - - - +
99A ILE* 1.3 56.5 + - - +
100A ASN* 4.3 12.3 - - + +
101A GLU* 2.4 30.5 - - + +
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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