Contacts of the strand formed by residues 73 - 78 (chain W) in PDB entry 1XDM
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 73 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27W LYS* 3.8 5.0 + - - -
28W GLY 3.6 4.7 - - - +
30W LEU* 4.1 23.6 - - + -
69W ILE* 2.7 39.5 + - + +
70W ASN* 3.5 23.4 - - - +
71W GLN 3.5 1.0 - - - -
72W SER* 1.3 90.3 - - - +
74W GLY* 1.3 62.9 + - - +
75W GLY 3.6 22.4 - - - +
76W VAL* 4.2 3.6 - - + -
102W ILE* 3.8 21.9 - - + +
299W PHE* 4.1 16.2 - - + -
305W LEU* 4.2 2.7 - - + -
327W PHE* 4.7 2.5 - - + -
331W ALA* 3.3 22.7 - - + -
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Residues in contact with GLY 74 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21W SER 4.2 1.1 - - - +
22W ILE* 3.5 32.6 - - - +
27W LYS* 4.0 17.1 - - - +
28W GLY 2.9 10.3 + - - -
73W ILE* 1.3 73.8 - - - +
75W GLY* 1.3 57.0 + - - +
101W GLY 5.0 1.0 - - - +
102W ILE* 3.9 6.7 - - - -
103W VAL* 3.2 26.7 + - - +
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Residues in contact with GLY 75 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22W ILE* 4.2 8.6 - - - +
28W GLY 3.9 2.6 + - - -
29W ILE* 3.4 8.9 - - - +
30W LEU 3.1 23.9 + - - -
73W ILE* 3.6 1.2 - - - +
74W GLY* 1.3 79.8 - - - +
76W VAL* 1.3 66.9 + - - +
102W ILE* 3.4 6.2 - - - +
103W VAL* 2.9 16.8 - - - -
144W PHE* 4.5 5.2 - - - -
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Residues in contact with VAL 76 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 3.4 30.3 - - + +
32W ALA* 4.5 5.8 - - + -
63W PHE* 4.2 13.9 - - + -
73W ILE* 4.2 3.6 - - + -
75W GLY* 1.3 81.0 - - - +
77W ILE* 1.3 68.2 + - - +
78W LEU* 3.8 21.3 + - + -
97W LEU* 4.1 20.9 - - + -
102W ILE* 3.9 16.4 - - + -
103W VAL 2.7 9.5 + - - -
104W VAL* 3.4 5.0 - - - +
105W GLY 2.5 33.1 + - - +
144W PHE* 4.1 1.4 - - - -
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Residues in contact with ILE 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29W ILE* 3.8 21.8 - - + -
30W LEU 3.4 2.6 + - - -
31W ALA* 4.3 12.8 - - + -
32W ALA 3.0 27.5 + - - +
33W ASP* 3.4 13.5 - - - +
76W VAL* 1.3 77.0 - - - +
78W LEU* 1.3 60.3 + - - +
105W GLY* 3.3 3.8 - - - -
106W ILE 3.5 23.6 - - - +
107W LYS 3.8 12.6 - - - +
144W PHE* 3.8 9.0 - - + -
146W LYS* 4.3 26.2 - - + +
185W ILE* 3.9 23.3 - - + -
229W LYS* 4.5 2.9 - - - +
300W SER* 4.2 10.5 - - - +
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Residues in contact with LEU 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32W ALA 3.7 7.9 - - - +
33W ASP* 3.6 5.2 - - - -
63W PHE* 3.3 39.0 - - + -
76W VAL* 3.8 13.0 - - + -
77W ILE* 1.3 75.2 - - - +
79W PHE* 1.3 61.6 + - - +
82W THR* 3.7 19.1 - - + +
83W LEU* 3.7 31.4 - - + +
93W PHE 5.6 0.2 - - - -
94W ARG* 5.0 7.6 - - - +
97W LEU* 4.7 6.5 - - + -
104W VAL* 3.6 27.4 - - + -
105W GLY 2.8 12.0 + - - +
106W ILE* 3.0 7.3 - - + +
107W LYS* 3.0 26.9 + - - +
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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