Contacts of the strand formed by residues 119 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG 3.4 1.4 - - - +
112B VAL* 3.3 6.9 - - - +
113B SER* 3.0 39.0 + - - -
117B PHE 3.7 2.8 + - - -
118B TRP* 1.3 90.0 - - - +
120B LEU* 1.3 60.6 + - - +
121B ASP* 2.6 32.8 + - - +
132B SER 4.1 5.2 + - - -
133B GLN* 5.5 2.9 - - - +
134B VAL 5.0 1.6 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.8 7.2 - - + -
57B PHE* 4.6 24.2 - - + -
67B VAL* 4.8 4.9 - - + -
111B ARG 3.5 8.1 - - - +
112B VAL* 4.7 5.4 - - + +
118B TRP* 4.1 12.5 - - + +
119B SER* 1.3 72.5 + - - +
121B ASP* 1.3 74.6 + - - +
122B PHE* 3.5 31.0 - - + -
131B GLY* 3.4 2.3 - - - -
132B SER* 2.9 48.8 + - - +
137B ASN* 4.4 8.7 - - - +
152B GLU* 4.0 9.4 - - - +
239B TYR* 3.7 21.8 - - - +
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 3.2 3.5 - - - -
111B ARG* 2.6 59.8 + - + +
113B SER* 4.6 5.4 + - - -
119B SER* 2.6 28.0 + - - +
120B LEU* 1.3 77.7 - - - +
122B PHE* 1.3 65.3 + - - +
123B LEU* 3.5 20.7 - - + +
128B ARG* 2.6 35.9 + - - +
130B THR 4.0 2.5 - - - -
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 4.5 5.6 - - + -
67B VAL* 3.7 24.5 - - + -
108B LEU* 4.5 7.9 - - + -
109B SER 3.2 8.1 - - - +
110B ALA* 3.7 26.0 - - + -
120B LEU* 3.5 22.7 - - + -
121B ASP* 1.3 73.8 - - - +
123B LEU* 1.3 61.1 + - - +
128B ARG* 3.4 4.7 - - - -
129B ILE* 3.0 30.9 + - + -
130B THR* 3.0 29.2 + - + +
131B GLY* 3.8 16.4 - - - -
154B LEU* 4.1 12.3 - - + -
239B TYR* 4.0 13.7 - - - -
241B VAL* 3.3 37.5 - - + -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 4.9 2.0 - - - +
107B ASN 3.4 1.4 - - - +
108B LEU* 3.3 9.8 - - - +
109B SER* 2.8 61.9 + - - +
111B ARG* 3.9 35.2 - - + +
121B ASP* 3.5 22.7 - - + +
122B PHE* 1.3 78.4 - - - +
124B ARG* 1.3 59.1 + - - +
125B ASN 4.0 0.2 - - - -
126B GLY* 3.7 15.5 - - - +
127B GLU 2.8 16.6 - - - +
128B ARG* 3.6 29.8 - - + +
129B ILE* 4.8 1.1 - - - -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASN* 3.3 8.5 - - + +
108B LEU* 5.4 0.4 - - + -
123B LEU* 1.3 73.2 - - - +
125B ASN* 1.3 89.8 + - - +
127B GLU* 2.6 23.6 + - + +
129B ILE* 3.2 41.1 - - + +
204B ARG* 2.9 27.5 + - - +
205B GLY 3.7 15.0 + - - -
206B TYR* 4.5 0.4 - - - +
243B ASP* 2.6 55.2 + - - +
244B GLY 4.1 0.4 - - - +
245B PRO* 4.0 25.0 + - - +
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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