Contacts of the strand formed by residues 63 - 70 (chain F) in PDB entry 1XIW
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 SER 63 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88E ASN* 3.4 18.5 + - - -
90E TYR* 4.3 4.0 - - - -
2F LYS* 3.7 22.7 + - - -
3F ILE* 3.7 20.8 + - - +
51F ARG* 3.3 2.5 - - - +
52F CYS* 2.7 35.2 + - - +
62F GLU* 1.3 78.8 - - - +
64F THR* 1.3 69.2 + - - +
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Residues in contact with THR 64 (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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88E ASN* 2.7 16.5 + - - +
89E PHE* 3.3 21.5 - - + -
90E TYR* 2.9 26.3 + - - +
3F ILE* 3.8 1.8 - - - -
23F VAL* 5.1 0.2 - - + -
49F ILE* 3.5 26.0 - - + -
50F TYR 3.4 13.9 - - - +
51F ARG* 3.8 25.9 + - + +
62F GLU* 5.7 0.9 + - - +
63F SER* 1.3 80.1 + - - +
65F VAL* 1.3 64.8 + - - +
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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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74E TYR* 4.6 9.4 - - + -
89E PHE* 4.3 3.6 - - - -
90E TYR* 3.4 12.3 - - + +
92E TYR* 4.1 19.1 - - + +
3F ILE* 3.4 38.6 - - + +
5F ILE* 4.1 19.7 - - + -
14F VAL* 4.3 7.9 - - + -
49F ILE* 3.3 1.9 - - - -
50F TYR* 2.8 47.5 + - + +
64F THR* 1.3 76.1 - - - +
66F GLN* 1.3 71.9 + - - +
67F VAL* 4.6 0.9 - - + -
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Residues in contact with GLN 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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14E PRO* 3.5 10.9 - - - +
15E TYR* 2.8 46.7 + - - -
17E VAL* 4.8 5.5 - - - +
89E PHE* 3.4 24.1 - - + -
90E TYR 2.8 12.5 + - - +
91E LEU* 3.4 25.1 - - + +
92E TYR 2.7 32.2 + - - -
48F GLY 3.2 12.1 - - - +
49F ILE* 3.8 8.1 - - + -
65F VAL* 1.3 74.5 - - - +
67F VAL* 1.3 61.1 - - - +
68F HIS* 4.9 7.1 + - - -
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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
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92E TYR* 3.8 6.5 - - + +
5F ILE* 4.0 27.4 - - + -
12F VAL* 4.9 0.4 - - + -
39F LEU* 4.0 19.3 - - + -
46F PRO* 3.7 9.2 - - + +
47F ARG* 3.2 6.1 - - - +
48F GLY 2.7 31.5 + - - +
50F TYR* 3.8 27.6 - - + -
65F VAL* 4.6 3.6 - - + -
66F GLN* 1.3 78.4 - - - +
68F HIS* 1.3 64.4 + - - +
69F TYR* 3.3 34.1 - - + -
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Residues in contact with HIS 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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17E VAL* 3.6 46.0 + - + +
19E ILE* 5.2 2.3 - - + +
91E LEU* 4.1 15.7 - - + -
92E TYR 3.0 13.9 + - - +
93E LEU* 3.7 12.3 - - + -
94E ARG* 3.1 27.0 + - - +
47F ARG* 3.7 44.8 + - - +
66F GLN* 4.9 7.4 + - - +
67F VAL* 1.3 77.1 + - - +
69F TYR* 1.3 66.8 + - - +
70F ARG* 4.5 7.7 - - + +
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Residues in contact with TYR 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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92E TYR* 3.6 18.2 - + - -
94E ARG* 3.3 32.1 - - + -
5F ILE* 3.9 3.3 - - - +
7F GLU* 2.8 21.5 + - - +
12F VAL* 3.5 28.4 - - + +
42F ARG* 3.2 35.4 - - + +
45F ASP* 3.3 14.6 - - - +
46F PRO* 3.2 35.2 + - + +
47F ARG* 2.9 24.2 + - - +
67F VAL* 3.3 34.1 - - + -
68F HIS* 1.3 74.3 - - - +
70F ARG* 1.3 60.7 + - - +
71F MET* 4.2 7.4 - - + -
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Residues in contact with ARG 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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19E ILE* 3.6 51.4 + - + +
21E GLY 5.1 3.6 + - - +
94E ARG 3.0 8.5 + - - -
95E ALA* 3.4 11.8 - - + -
96E ARG 2.8 48.6 + - - +
97E VAL* 4.2 5.5 - - - +
98E CYS* 4.3 9.7 + - - +
45F ASP* 3.5 7.6 - - - +
47F ARG* 3.5 18.2 - - - +
68F HIS* 4.5 7.0 - - + +
69F TYR* 1.3 75.8 - - - +
71F MET* 1.3 60.9 + - - +
72F CYS* 3.3 20.6 - - - +
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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