Contacts of the strand formed by residues 119 - 124 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ARG 3.3 1.6 - - - +
112E VAL* 3.2 6.8 - - - +
113E SER* 2.8 47.5 + - - -
117E PHE* 3.5 3.0 + - - -
118E TRP* 1.3 90.5 - - - +
120E LEU* 1.3 60.6 + - - +
121E ASP* 3.0 27.2 + - - -
132E SER 4.2 4.9 + - - -
133E GLN* 5.5 1.3 - - - +
134E VAL 5.3 0.9 - - - +
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E LEU* 4.8 8.1 - - + -
57E PHE* 4.3 23.3 - - + -
67E VAL* 4.7 4.5 - - + -
69E ILE* 5.5 0.4 - - + -
111E ARG 3.6 9.6 - - - +
112E VAL* 4.3 13.2 - - + -
118E TRP* 4.4 10.4 - - + +
119E SER* 1.3 74.1 + - - +
121E ASP* 1.3 75.8 + - - +
122E PHE* 4.0 24.0 - - + -
131E GLY* 3.3 0.4 - - - -
132E SER* 2.8 49.3 + - - +
137E ASN* 4.6 7.9 - - - +
152E GLU* 4.1 8.3 - - - +
239E TYR* 3.5 24.5 - - - +
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Residues in contact with ASP 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ALA* 3.4 2.6 - - - -
111E ARG* 2.6 66.6 + - - +
113E SER* 4.6 2.9 + - - -
119E SER* 3.0 21.4 + - - -
120E LEU* 1.3 78.1 - - - +
122E PHE* 1.3 63.3 + - - +
123E LEU* 3.4 22.6 - - + +
128E ARG* 2.9 38.9 + - - +
130E THR 4.0 2.2 - - - -
132E SER 5.4 0.2 - - - +
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Residues in contact with PHE 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E VAL* 4.5 7.0 - - + -
67E VAL* 3.8 19.1 - - + -
108E LEU* 4.6 7.6 - - + -
109E SER 3.2 11.9 - - - +
110E ALA* 3.9 19.5 - - + -
120E LEU* 4.0 18.2 - - + -
121E ASP* 1.3 72.2 - - - +
123E LEU* 1.3 60.1 + - - +
128E ARG* 3.5 4.2 - - - -
129E ILE* 3.1 29.6 + - + +
130E THR* 2.9 27.5 + - + +
131E GLY* 3.8 16.6 - - - -
154E LEU* 3.9 14.1 - - + -
239E TYR* 3.5 36.3 - + - -
241E VAL* 3.8 27.6 - - + -
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Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLU* 4.4 3.4 - - - +
107E ASN 3.4 1.7 - - - +
108E LEU* 3.3 10.0 - - - +
109E SER* 2.9 49.8 + - - +
111E ARG* 3.7 35.2 - - + +
121E ASP* 3.4 31.2 - - + +
122E PHE* 1.3 76.2 - - - +
124E ARG* 1.3 58.6 + - - +
125E ASN 4.0 0.2 - - - -
126E GLY* 3.9 16.6 - - - +
127E GLU 3.1 15.0 - - - +
128E ARG* 3.6 31.6 - - + +
129E ILE* 4.9 0.7 - - - -
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Residues in contact with ARG 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ASN* 3.4 8.1 - - + +
108E LEU* 4.7 0.4 - - - +
123E LEU* 1.3 71.0 - - - +
125E ASN* 1.3 80.1 + - - +
127E GLU* 2.6 37.3 + - + +
129E ILE* 3.5 35.3 - - + +
204E ARG* 2.8 32.9 + - - +
205E GLY 3.4 16.6 + - - -
243E ASP* 2.5 48.7 + - - +
245E PRO* 3.6 29.1 + - - +
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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