Contacts of the strand formed by residues 120 - 124 (chain A) 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 LEU 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 5.1 5.6 - - + -
57A PHE* 4.4 20.9 - - + -
67A VAL* 4.9 4.5 - - + -
69A ILE* 5.5 0.4 - - + -
110A ALA* 4.5 3.4 - - + -
111A ARG 3.5 6.3 - - - +
112A VAL* 4.4 12.3 - - + +
118A TRP* 4.4 12.5 - - + +
119A SER* 1.3 75.2 + - - +
121A ASP* 1.3 73.3 + - - +
122A PHE* 3.8 28.7 - - + -
131A GLY* 3.3 3.1 - - - -
132A SER* 2.8 49.9 + - - +
137A ASN* 4.6 6.5 - - - +
152A GLU* 4.2 7.6 - - - +
239A TYR* 3.8 22.4 - - - +
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Residues in contact with ASP 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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110A ALA* 3.4 1.7 - - - -
111A ARG* 2.6 67.5 + - - +
113A SER* 4.6 3.5 + - - -
119A SER* 3.4 22.3 + - - -
120A LEU* 1.3 75.2 - - - +
122A PHE* 1.3 63.0 + - - +
123A LEU* 3.1 19.6 - - + +
128A ARG* 2.9 43.3 + - - -
130A THR 4.0 2.5 - - - -
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Residues in contact with PHE 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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65A VAL* 4.4 5.4 - - + -
67A VAL* 3.8 21.1 - - + -
108A LEU* 4.6 8.1 - - + -
109A SER 3.2 6.5 - - - +
110A ALA* 3.9 22.2 - - + -
120A LEU* 3.8 20.9 - - + -
121A ASP* 1.3 71.2 - - - +
123A LEU* 1.3 62.1 + - - +
128A ARG* 3.4 4.3 - - - -
129A ILE* 3.0 31.1 + - + -
130A THR* 3.0 31.4 + - + +
131A GLY* 3.6 18.4 - - - -
154A LEU* 3.9 14.8 - - + -
239A TYR* 3.7 23.8 - - - -
241A VAL* 3.5 33.2 - - + -
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Residues in contact with LEU 123 (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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102A GLU* 5.7 2.0 - - - +
107A ASN 3.3 1.0 - - - +
108A LEU* 3.3 8.6 - - - +
109A SER* 2.7 53.2 + - - +
111A ARG* 4.1 29.6 - - + +
121A ASP* 3.1 36.1 - - + +
122A PHE* 1.3 76.9 - - - +
124A ARG* 1.3 60.8 + - - +
125A ASN 4.0 0.4 - - - -
126A GLY* 3.2 26.2 - - - +
127A GLU 3.1 7.0 - - - +
128A ARG* 3.1 39.9 - - + +
129A ILE* 4.9 1.1 - - - -
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Residues in contact with ARG 124 (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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107A ASN* 3.2 8.1 - - + +
108A LEU* 4.7 0.9 - - - +
123A LEU* 1.3 71.2 - - - +
125A ASN* 1.3 88.2 + - - +
127A GLU* 2.8 22.2 + - + +
129A ILE* 3.2 40.8 - - + +
204A ARG* 2.8 27.9 + - - +
205A GLY* 3.2 19.2 + - - -
243A ASP* 2.4 57.8 + - - +
245A PRO* 3.8 28.1 + - - +
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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