Contacts of the strand formed by residues 64 - 70 (chain F) 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 ILE 64 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F SER* 2.8 29.1 + - - -
60F PRO* 3.4 11.6 - - + +
61F GLN* 2.9 38.1 + - + +
62F GLU 4.4 3.1 - - - +
63F GLY* 1.3 83.5 - - - +
65F VAL* 1.3 63.1 + - - +
105F SER* 4.2 0.6 + - - -
240F PHE* 3.6 38.1 - - + -
241F VAL 3.4 5.8 - - - +
242F ILE* 3.8 23.6 - - + -
253F ARG* 3.9 10.8 - - + +
257F PHE* 3.9 24.7 - - + -
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Residues in contact with VAL 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F PHE* 4.4 5.2 - - + -
58F PHE 3.6 2.7 - - - -
63F GLY 4.2 0.2 - - - -
64F ILE* 1.3 75.7 - - - +
66F GLY* 1.3 69.7 + - - +
67F VAL* 3.8 5.3 + - + +
103F PHE* 4.0 26.5 - - + -
105F SER* 4.4 5.2 - - - -
108F LEU* 3.8 42.0 - - + +
109F SER* 4.6 4.7 - - - -
110F ALA* 3.9 25.4 - - + -
122F PHE* 4.5 3.1 - - + -
239F TYR 3.9 0.3 - - - +
240F PHE* 3.6 1.8 - - - -
241F VAL* 3.0 36.0 + - + +
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Residues in contact with GLY 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F PHE* 3.4 5.4 - - - -
58F PHE* 2.8 48.0 + - - -
64F ILE 3.9 0.6 + - - -
65F VAL* 1.3 73.3 - - - +
67F VAL* 1.3 62.3 + - - +
239F TYR 3.5 1.6 - - - -
240F PHE* 3.3 33.4 - - - -
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F LEU* 5.4 2.2 - - + -
56F ARG 3.6 3.1 - - - +
57F PHE* 3.7 31.6 - - + -
58F PHE* 4.2 0.4 - - - -
65F VAL* 4.3 4.0 - - + +
66F GLY* 1.3 77.3 - - - -
68F ARG* 1.3 61.3 + - - +
69F ILE* 3.9 18.4 - - + -
120F LEU* 4.8 3.4 - - + -
122F PHE* 3.7 33.2 - - + -
237F LEU 3.4 1.9 - - - +
238F GLU* 3.1 6.1 - - - +
239F TYR* 2.8 64.5 + - + +
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Residues in contact with ARG 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F THR 3.2 7.8 - - - +
55F LEU* 3.5 0.4 - - - -
56F ARG* 3.0 51.8 + - + +
58F PHE* 4.4 5.4 - - + -
67F VAL* 1.3 72.8 - - - +
69F ILE* 1.3 60.3 + - - +
70F GLU* 3.2 32.3 + - - +
77F ASN* 4.7 4.0 + - - -
236F TYR* 3.4 57.9 + - + -
237F LEU 3.4 2.9 - - - -
238F GLU* 3.1 35.5 + - + +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F PRO* 5.4 3.8 - - + -
53F PHE* 4.1 16.6 - - + -
54F THR 3.9 2.9 - - - -
55F LEU* 4.1 25.1 - - + -
67F VAL* 3.9 16.2 - - + -
68F ARG* 1.3 73.6 - - - +
70F GLU* 1.3 59.6 + - - +
120F LEU* 5.3 0.7 - - + -
137F ASN* 3.5 33.4 - - + +
138F GLY* 5.5 1.8 - - - -
150F MET* 3.2 25.8 - - + +
151F PHE 5.1 0.9 - - - +
152F GLU* 3.8 13.2 - - - +
237F LEU* 2.8 47.6 + - + +
239F TYR* 4.3 11.7 - - + -
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F LEU 4.3 0.5 - - - +
53F PHE* 3.8 10.3 - - - -
54F THR* 3.1 45.3 + - - +
56F ARG* 5.9 0.9 + - - -
68F ARG* 3.2 38.1 + - + +
69F ILE* 1.3 73.6 - - - +
71F HIS* 1.3 63.7 + - - +
72F PHE 4.2 2.1 - - - +
73F GLN* 3.1 47.2 - - + +
77F ASN* 5.7 0.3 - - - +
150F MET* 4.8 0.2 - - - -
235F GLU 3.5 2.9 - - - +
236F TYR* 3.2 22.3 - - + +
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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