Contacts of the strand formed by residues 99 - 103 (chain C) in PDB entry 1XWD
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 GLU 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A THR* 3.6 7.1 + - - -
88A TYR* 2.6 25.8 + - - +
96B VAL* 5.6 0.2 - - - +
73C GLU 3.2 3.0 + - - +
74C LYS* 3.3 46.0 + - + +
75C ILE 3.1 24.5 + - - +
76C GLU* 5.9 1.0 - - - +
97C LEU* 3.8 3.1 - - - +
98C HIS* 1.3 82.4 - - + +
100C ILE* 1.3 65.8 + - - +
101C ARG* 2.5 35.4 - - + +
122C LEU* 4.3 0.4 - - - +
124C TYR* 3.2 27.6 - - + -
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Residues in contact with ILE 100 (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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75C ILE* 3.7 8.7 - - + +
77C ILE* 5.5 0.4 - - + -
91C PHE* 3.9 36.1 - - + -
97C LEU* 3.7 30.7 - - + -
99C GLU* 1.3 78.7 - - - +
101C ARG* 1.3 63.7 + - - +
102C ILE* 4.1 14.4 - - + -
116C PHE* 3.8 25.8 - - + -
119C LEU* 4.1 9.2 - - + -
122C LEU* 4.1 9.4 - - + -
124C TYR 3.1 7.6 + - - +
125C LEU* 3.6 19.8 + - + -
126C LEU* 2.8 28.8 + - - +
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Residues in contact with ARG 101 (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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86A THR* 3.8 17.8 - - - +
87A CYS 4.9 2.8 + - - -
88A TYR* 4.9 0.2 - - - -
94B CYS 4.6 3.6 + - - -
95B THR* 3.7 6.5 - - - +
96B VAL* 3.4 38.9 - - - +
75C ILE 2.9 13.9 + - - +
76C GLU* 3.5 14.1 + - - +
77C ILE* 2.7 34.3 + - - +
99C GLU* 2.5 32.7 - - - +
100C ILE* 1.3 76.4 - - - +
102C ILE* 1.3 60.1 + - - +
103C GLU* 2.9 41.1 + - - +
124C TYR* 3.8 12.0 + - + -
126C LEU* 3.5 32.1 - - + +
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Residues in contact with ILE 102 (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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77C ILE* 3.4 27.6 - - + +
83C LEU* 5.2 0.7 - - + -
86C ILE* 3.7 27.6 - - + -
91C PHE* 4.6 14.4 - - + -
100C ILE* 4.2 11.2 - - + -
101C ARG* 1.3 75.1 - - - +
103C GLU* 1.3 61.8 + - - +
105C ALA* 4.9 7.9 - - + -
108C LEU* 4.0 22.0 - - + -
111C ILE* 4.7 4.5 - - + -
116C PHE* 4.9 2.9 - - + -
126C LEU 2.8 13.3 + - - +
127C ILE* 3.4 25.6 - - + -
128C SER 3.1 24.4 + - - +
130C THR* 4.5 8.3 - - - +
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Residues in contact with GLU 103 (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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95B THR* 3.1 30.8 - - - +
76C GLU* 4.0 12.7 - - - +
77C ILE* 2.7 20.2 + - - +
78C SER* 4.0 10.8 + - - +
79C GLN 3.1 12.8 + - - -
80C ASN* 4.6 0.9 + - - +
101C ARG* 2.9 47.8 + - - +
102C ILE* 1.3 78.3 - - - +
104C LYS* 1.3 82.9 + - - +
105C ALA* 3.4 5.1 + - - +
126C LEU* 3.7 18.2 - - + -
128C SER* 3.5 12.8 - - - +
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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