Contacts of the strand formed by residues 64 - 70 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER* 2.6 32.6 + - - -
60C PRO* 3.5 20.8 - - + +
61C GLN* 2.8 27.8 + - + +
62C GLU 4.3 2.0 - - - +
63C GLY* 1.3 83.0 - - - +
65C VAL* 1.3 64.3 + - - +
105C SER* 4.2 1.0 + - - -
240C PHE* 3.6 22.7 - - + -
241C VAL 3.6 7.0 - - - +
242C ILE* 3.9 25.8 - - + -
253C ARG* 4.3 10.3 - - + +
257C PHE* 3.8 37.2 - - + -
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PHE* 4.3 1.8 - - + -
58C PHE 3.6 2.2 - - - -
64C ILE* 1.3 74.8 - - - +
66C GLY* 1.3 70.5 + - - +
67C VAL* 3.8 10.7 + - + +
103C PHE* 4.2 24.0 - - + -
105C SER* 4.4 6.1 - - - -
108C LEU* 3.6 42.3 - - + +
109C SER* 4.5 4.7 - - - -
110C ALA* 4.0 24.7 - - + +
122C PHE* 4.3 6.1 - - + -
239C TYR 3.9 0.2 - - - +
240C PHE* 3.5 3.9 - - - -
241C VAL* 3.1 31.3 + - + +
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Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 3.2 8.1 - - - -
58C PHE* 2.7 50.5 + - - -
60C PRO* 4.4 0.2 - - - +
64C ILE 4.0 0.6 + - - -
65C VAL* 1.3 74.7 - - - +
67C VAL* 1.3 60.8 + - - +
239C TYR 3.5 1.3 - - - -
240C PHE* 3.5 30.4 - - - -
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 5.2 2.0 - - + -
56C ARG 3.6 3.4 - - - +
57C PHE* 3.6 36.3 - - + -
58C PHE* 4.1 0.8 - - - -
65C VAL* 4.2 5.6 - - + +
66C GLY* 1.3 75.6 - - - -
68C ARG* 1.3 60.7 + - - +
69C ILE* 3.9 18.8 - - + -
120C LEU* 4.8 2.9 - - + -
122C PHE* 3.7 27.1 - - + -
237C LEU 3.4 3.3 - - - +
238C GLU* 3.3 4.8 - - - +
239C TYR* 2.8 64.5 + - + +
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C THR 3.3 3.8 - - - +
55C LEU* 3.3 2.6 - - - -
56C ARG* 2.9 57.4 + - + +
58C PHE* 4.4 5.4 - - + -
66C GLY 4.1 0.4 - - - -
67C VAL* 1.3 72.0 - - - +
69C ILE* 1.3 61.8 + - - +
70C GLU* 3.4 33.7 + - - +
77C ASN* 4.7 5.7 + - - +
236C TYR* 3.3 56.4 + - + -
237C LEU 3.5 2.7 - - - -
238C GLU* 2.8 44.3 + - + +
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Residues in contact with ILE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 5.6 4.0 - - + -
53C PHE* 4.4 14.1 - - + -
54C THR 3.7 3.1 - - - +
55C LEU* 3.9 29.2 - - + +
67C VAL* 3.9 18.2 - - + -
68C ARG* 1.3 73.6 - - - +
70C GLU* 1.3 59.8 + - - +
120C LEU* 5.3 0.7 - - + -
137C ASN* 3.8 19.7 - - + +
138C GLY* 5.7 2.9 - - - +
150C MET* 3.3 24.6 - - + +
151C PHE 5.2 0.7 - - - +
152C GLU* 3.6 24.0 - - - +
236C TYR* 3.3 1.8 - - - -
237C LEU* 2.8 49.2 + - + +
239C TYR* 4.4 5.6 - - + -
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU 4.3 0.2 - - - +
53C PHE* 3.8 10.6 - - - -
54C THR* 3.0 49.5 + - - +
56C ARG* 5.5 5.2 + - - +
68C ARG* 3.4 34.1 + - + +
69C ILE* 1.3 75.9 - - - +
71C HIS* 1.3 65.1 + - - +
72C PHE 4.3 2.0 - - - +
73C GLN* 3.0 40.6 + - + +
150C MET* 4.8 0.2 - - - -
235C GLU 3.8 2.5 - - - +
236C TYR* 3.4 19.3 - - + +
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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