Contacts of the strand formed by residues 119 - 124 (chain C) in PDB entry 1XSK
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 SER 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ARG 3.4 0.9 - - - +
112C VAL* 3.2 9.7 - - - +
113C SER* 2.9 43.5 + - - -
117C PHE 3.6 2.2 + - - -
118C TRP* 1.3 90.6 - - - +
120C LEU* 1.3 61.5 + - - +
121C ASP* 2.9 25.0 + - - -
132C SER 4.2 5.0 + - - -
133C GLN* 5.4 2.3 - - - +
134C VAL 5.2 0.9 - - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 4.7 9.2 - - + -
57C PHE* 4.3 29.6 - - + -
67C VAL* 4.8 2.9 - - + -
69C ILE* 5.3 0.2 - - + -
110C ALA* 4.5 2.7 - - + -
111C ARG 3.5 6.3 - - - +
112C VAL* 4.5 5.8 - - + -
118C TRP* 4.2 11.6 - - + +
119C SER* 1.3 74.5 + - - +
121C ASP* 1.3 75.7 + - - +
122C PHE* 3.9 24.5 - - + -
128C ARG* 4.3 0.2 + - - -
131C GLY* 3.4 1.7 - - - -
132C SER* 2.9 48.1 + - - +
137C ASN* 4.4 7.2 - - - +
152C GLU* 4.2 9.4 - - - +
239C TYR* 3.8 21.5 - - - +
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ALA* 3.3 2.9 - - - -
111C ARG* 2.6 71.0 + - - +
113C SER* 4.4 3.3 + - - -
119C SER* 2.9 27.1 + - - -
120C LEU* 1.3 75.7 - - - +
122C PHE* 1.3 63.6 + - - +
123C LEU* 3.3 17.1 - - + +
128C ARG* 2.8 35.4 + - - +
130C THR 4.1 3.6 - - - -
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Residues in contact with PHE 122 (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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65C VAL* 4.3 5.8 - - + -
67C VAL* 3.7 19.1 - - + -
108C LEU* 4.6 8.1 - - + -
109C SER 3.2 8.3 - - - +
110C ALA* 3.8 26.0 - - + -
120C LEU* 3.9 17.0 - - + -
121C ASP* 1.3 71.9 - - - +
123C LEU* 1.3 62.8 + - - +
128C ARG* 3.4 4.9 - - - -
129C ILE* 3.1 30.4 + - + -
130C THR* 3.0 30.0 + - + +
131C GLY* 3.8 16.8 - - - -
154C LEU* 4.0 12.1 - - + -
239C TYR* 3.7 24.5 - - - -
241C VAL* 3.4 37.2 - - + -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLU* 5.4 1.8 - - - +
107C ASN 3.3 0.7 - - - +
108C LEU* 3.3 10.0 - - - +
109C SER* 2.7 51.8 + - - +
111C ARG* 3.8 37.2 - - + +
121C ASP* 3.3 25.1 - - + +
122C PHE* 1.3 80.1 - - - +
124C ARG* 1.3 60.7 + - - +
125C ASN 4.0 0.4 - - - -
126C GLY* 4.0 22.2 - - - +
127C GLU 2.9 7.9 - - - +
128C ARG* 3.3 38.4 - - + +
129C ILE* 4.9 1.1 - - - -
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Residues in contact with ARG 124 (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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107C ASN* 3.2 7.0 - - + +
108C LEU* 5.4 0.4 - - + -
123C LEU* 1.3 72.5 - - - +
125C ASN* 1.3 89.6 + - - +
127C GLU* 2.7 26.9 + - + +
129C ILE* 3.3 38.3 - - + +
204C ARG* 2.8 29.7 + - - +
205C GLY* 3.0 19.1 + - - -
243C ASP* 2.4 51.6 + - - +
244C GLY 3.7 1.4 - - - +
245C PRO* 3.7 26.2 + - - +
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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