Contacts of the strand formed by residues 103 - 107 (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 VAL 103 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18W ILE* 4.1 10.5 - - + -
21W SER* 4.1 22.9 - - - +
22W ILE* 4.3 7.2 - - + -
74W GLY 3.2 20.2 + - - +
75W GLY* 2.9 4.4 - - - -
76W VAL* 2.7 26.3 + - - +
101W GLY 4.7 5.6 - - - +
102W ILE* 1.3 74.3 - - - +
104W VAL* 1.3 64.0 + - - +
143W ASP* 3.2 42.0 - - + +
144W PHE* 4.3 6.5 - - + -
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Residues in contact with VAL 104 (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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76W VAL 3.4 3.8 - - - +
78W LEU* 3.6 30.5 - - + -
83W LEU* 4.7 10.8 - - + -
94W ARG* 3.7 23.3 - - + +
97W LEU* 3.7 29.4 - - + -
98W LYS* 4.7 4.0 - - + +
102W ILE 4.0 2.2 - - - +
103W VAL* 1.3 79.6 - - - +
105W GLY* 1.3 64.9 + - - +
141W GLY 4.1 14.6 + - - +
142W VAL* 3.3 6.2 - - + +
143W ASP* 3.0 29.0 + - - -
144W PHE* 3.3 7.5 - - - -
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Residues in contact with GLY 105 (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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76W VAL 2.5 17.6 + - - +
77W ILE* 3.6 6.7 - - - -
78W LEU* 2.8 20.8 + - - +
104W VAL* 1.3 81.2 - - - +
106W ILE* 1.3 65.2 + - - +
142W VAL* 3.8 2.0 - - - -
144W PHE* 3.0 32.5 - - - -
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Residues in contact with ILE 106 (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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77W ILE* 3.5 7.7 - - - +
78W LEU* 3.0 33.0 - - + +
79W PHE 3.8 16.2 - - - +
80W HIS* 4.0 1.3 - - - +
83W LEU* 4.0 16.6 - - + -
105W GLY* 1.3 76.9 - - - +
107W LYS* 1.3 62.8 + - - +
108W LEU* 2.9 29.3 + - + +
137W TYR* 3.1 49.4 - - + +
142W VAL* 3.6 18.2 - - + -
144W PHE 3.0 13.7 + - - +
145W GLY* 3.6 1.2 - - - -
146W LYS 3.4 13.7 + - - -
182W LEU* 5.3 2.0 - - + -
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Residues in contact with LYS 107 (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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33W ASP* 3.7 33.8 + - + +
34W GLU* 5.4 0.8 - - - +
35W SER* 4.9 12.5 + - - +
77W ILE* 3.8 2.8 - - - +
78W LEU 3.0 19.7 + - - +
79W PHE* 3.6 34.9 - - + -
80W HIS* 4.9 3.3 + - - +
106W ILE* 1.3 72.7 - - - +
108W LEU* 1.3 64.9 + - - +
133W ARG* 4.5 5.7 + - - -
137W TYR* 5.0 0.7 + - - -
146W LYS* 4.4 13.9 - - + -
148W ARG* 3.1 37.4 - - - +
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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