Contacts of the strand formed by residues 117 - 122 (chain A) in PDB entry 1XUD
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 ASN 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LYS* 3.4 25.4 - - + +
116A MET* 1.3 80.3 - - - +
118A LEU* 1.3 60.3 + - - +
119A THR* 5.3 2.8 - - + +
152A ASN* 3.0 35.4 - - + +
154A THR* 6.0 1.8 - - - +
162A ASP* 4.0 1.0 - - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TRP* 3.7 33.9 - - + +
115A LYS* 3.8 27.6 - - - +
116A MET 4.3 4.0 - - - +
117A ASN* 1.3 81.3 - - - +
119A THR* 1.3 65.9 + - - +
151A LEU* 4.3 10.5 - - + -
152A ASN 2.8 17.1 + - - +
153A PHE* 3.3 30.9 - - + -
154A THR* 2.9 24.9 + - - -
162A ASP* 3.4 15.3 - - + +
163A ILE* 4.9 4.0 - - + -
228A LEU* 3.7 20.6 - - + -
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASN* 5.3 2.7 - - + +
118A LEU* 1.3 79.6 - - - +
120A TYR* 1.3 62.4 + - - +
153A PHE* 5.7 1.3 - - - -
154A THR* 3.1 20.6 - - - +
156A LEU* 3.8 25.9 - - + +
160A ILE 4.6 0.7 + - - -
161A ALA* 3.3 7.3 - - - -
162A ASP* 2.9 34.9 + - - +
163A ILE* 2.9 25.6 + - - +
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Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A THR* 1.3 75.2 - - - +
121A ARG* 1.3 63.0 + - - +
122A ILE* 4.4 15.0 - - + -
135A GLU 5.1 1.7 + - - -
138A PHE* 4.9 4.0 - - + -
139A LYS* 4.2 23.7 + - - +
142A PHE* 3.3 49.4 - + + -
153A PHE* 4.2 20.2 - - + -
154A THR 3.0 13.7 + - - -
155A ARG* 3.5 43.9 - - + +
156A LEU* 2.7 30.7 + - - +
161A ALA* 3.5 3.6 - - - -
163A ILE* 3.2 16.4 - - + +
165A ILE* 3.9 11.0 - - + -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 1.3 78.4 - - - +
122A ILE* 1.3 68.8 + - - +
123A VAL* 3.3 30.0 + - + +
155A ARG* 5.3 0.2 - - - -
156A LEU* 3.5 18.6 - - + +
157A HIS 4.0 7.5 + - - -
158A ASP* 3.7 25.0 - - - +
159A GLY* 2.7 43.3 + - - +
161A ALA* 3.7 13.4 - - + +
163A ILE 3.1 7.1 + - - -
164A MET* 3.5 24.2 - - - +
165A ILE* 2.8 30.6 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 4.4 18.8 - - + -
121A ARG* 1.3 77.4 + - - +
123A VAL* 1.3 61.3 + - - +
124A ASN 3.4 20.2 - - - +
125A TYR* 3.5 32.4 + - + +
134A VAL* 4.5 0.2 - - + -
135A GLU* 3.7 33.9 - - + +
138A PHE* 3.8 39.7 - - + -
155A ARG* 4.1 17.4 + - - +
156A LEU 4.3 2.4 + - - -
157A HIS* 5.2 2.9 - - - +
165A ILE* 3.8 7.6 - - + +
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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