Contacts of the strand formed by residues 28 - 31 (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 GLY 28 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22W ILE 4.3 3.4 - - - -
27W LYS* 1.3 75.8 - - - +
29W ILE* 1.3 66.6 + - - -
72W SER 3.9 1.8 + - - -
73W ILE* 3.6 5.2 - - - +
74W GLY* 2.9 24.3 + - - -
268W CYS* 5.2 0.7 - - - -
298W SER* 2.9 16.4 - - - -
299W PHE* 3.2 25.0 - - - -
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Residues in contact with ILE 29 (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* 3.4 32.5 - - + -
28W GLY* 1.3 72.2 - - - -
30W LEU* 1.3 64.7 + - - +
75W GLY 3.4 14.6 - - - +
77W ILE* 3.8 31.0 - - + -
144W PHE* 4.1 4.7 - - + -
185W ILE* 3.6 27.8 - - + -
227W LEU* 3.9 12.8 - - + -
268W CYS* 4.3 12.8 - - + -
299W PHE* 2.8 23.0 + - - +
300W SER* 2.9 38.4 + - - +
301W TYR 3.4 2.9 + - - -
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Residues in contact with LEU 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W GLY 4.0 1.8 + - - -
29W ILE* 1.3 71.0 - - - +
31W ALA* 1.3 60.9 + - - +
32W ALA* 3.3 20.8 + - + -
62W LEU* 4.7 8.7 - - + -
63W PHE* 4.7 6.5 - - + -
73W ILE* 4.1 13.5 - - + +
75W GLY 3.1 7.1 + - - -
76W VAL* 3.4 43.2 - - + +
77W ILE 3.4 1.7 + - - -
301W TYR 3.7 4.3 - - - +
305W LEU* 3.4 38.1 - - + -
306W GLN* 4.1 19.3 - - + +
327W PHE* 3.5 28.9 - - + -
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Residues in contact with ALA 31 (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 3.4 2.0 + - - -
30W LEU* 1.3 69.3 - - - +
32W ALA* 1.3 60.0 + - - +
33W ASP* 3.5 17.0 + - - +
34W GLU* 4.4 2.4 - - - +
77W ILE* 4.3 12.8 - - + -
146W LYS* 4.4 0.4 - - - +
229W LYS* 4.1 12.3 - - - +
300W SER* 3.8 22.0 - - - +
301W TYR 2.9 16.0 + - - +
302W GLY* 3.3 11.7 - - - +
303W ARG* 4.8 5.9 + - - +
306W GLN* 3.1 15.7 + - - -
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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