Contacts of the strand formed by residues 119 - 124 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ARG 3.4 1.4 - - - +
112F VAL* 3.2 8.8 - - - +
113F SER* 3.0 41.8 + - - -
117F PHE 3.7 1.9 + - - -
118F TRP* 1.3 90.6 - - - +
120F LEU* 1.3 61.2 + - - +
121F ASP* 3.0 24.4 + - - -
128F ARG* 5.5 0.3 + - - -
132F SER 4.3 4.4 + - - -
133F GLN* 5.4 3.1 - - - +
134F VAL 5.1 1.1 - - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 5.0 6.7 - - + -
57F PHE* 4.5 18.4 - - + -
67F VAL* 4.8 5.2 - - + -
69F ILE* 5.3 0.2 - - + -
111F ARG 3.4 7.0 - - - +
112F VAL* 4.3 13.7 - - + +
118F TRP* 4.2 10.0 - - + +
119F SER* 1.3 74.4 + - - +
121F ASP* 1.3 76.9 + - - +
122F PHE* 3.5 30.5 - - + -
128F ARG* 4.3 0.3 + - - -
131F GLY* 3.4 0.3 - - - -
132F SER* 2.9 49.7 + - - +
137F ASN* 4.5 8.3 - - - +
152F GLU* 4.1 10.1 - - - +
239F TYR* 3.7 21.8 - - - +
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Residues in contact with ASP 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F ALA* 3.3 4.3 - - - -
111F ARG* 2.7 63.3 + - + +
113F SER* 4.6 2.9 + - - -
119F SER* 3.0 22.2 + - - -
120F LEU* 1.3 78.2 - - - +
122F PHE* 1.3 62.8 + - - +
123F LEU* 3.5 22.1 - - + +
128F ARG* 2.4 38.9 + - - +
130F THR 4.0 2.7 - - - -
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Residues in contact with PHE 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F VAL* 4.5 6.7 - - + -
67F VAL* 3.7 22.7 - - + -
108F LEU* 4.6 3.6 - - + -
109F SER 3.3 6.1 - - - +
110F ALA* 3.9 23.3 - - + -
120F LEU* 3.5 22.9 - - + -
121F ASP* 1.3 72.9 - - - +
123F LEU* 1.3 60.2 + - - +
128F ARG* 3.6 2.6 - - - -
129F ILE* 3.1 35.5 + - + +
130F THR* 3.0 29.7 + - + +
131F GLY* 3.9 16.6 - - - -
154F LEU* 4.0 13.7 - - + -
239F TYR* 3.5 23.6 - - - -
241F VAL* 3.6 34.8 - - + -
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Residues in contact with LEU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F GLU* 4.9 1.8 - - - +
107F ASN 3.4 1.2 - - - +
108F LEU* 3.3 11.5 - - - +
109F SER* 2.9 48.2 + - - +
111F ARG* 3.8 37.2 - - + +
121F ASP* 3.5 29.4 - - + +
122F PHE* 1.3 75.6 - - - +
124F ARG* 1.3 60.9 + - - +
125F ASN 3.8 0.7 - - - -
126F GLY* 4.0 23.6 - - - +
127F GLU 3.1 7.0 - - - +
128F ARG* 3.5 35.0 - - + +
129F ILE* 4.9 0.4 - - - -
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Residues in contact with ARG 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ASN* 3.4 5.6 - - + +
108F LEU* 5.0 0.4 - - + -
123F LEU* 1.3 71.6 - - - +
125F ASN* 1.3 89.4 + - - +
127F GLU* 2.6 23.7 + - + +
129F ILE* 3.6 40.0 - - + +
204F ARG* 2.8 27.3 + - - +
205F GLY 3.2 20.8 + - - -
243F ASP* 2.6 56.2 + - - +
245F PRO* 3.5 29.9 + - - +
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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