Contacts of the strand formed by residues 132 - 136 (chain A) in PDB entry 1SXQ
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 ILE 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A MET* 5.2 0.4 - - + -
93A LYS* 4.8 1.8 - - - -
94A ILE* 3.4 25.6 - - + +
96A TYR* 4.0 25.6 - - + -
105A PHE* 3.4 46.2 - - + -
128A ILE* 4.5 6.1 - - + -
130A SER 3.6 6.7 - - - +
131A PRO* 1.3 79.6 - - - +
133A LYS* 1.3 65.3 + - - +
134A VAL* 4.5 3.1 - - + -
153A ASN* 2.9 27.3 + - - +
154A VAL* 3.5 17.7 - - + +
155A ILE* 3.2 24.3 + - - +
156A GLU 3.6 4.5 + - - +
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LYS* 4.1 9.1 - - + +
94A ILE 2.8 13.2 + - - +
95A TYR* 3.5 18.5 - - + -
96A TYR 2.9 24.3 + - - -
131A PRO 4.3 0.2 - - - -
132A ILE* 1.3 73.5 - - - +
134A VAL* 1.3 68.1 + - - +
135A ILE* 3.6 6.3 + - + +
156A GLU* 3.5 42.3 + - + +
157A PHE 5.2 0.2 - - - -
158A GLU* 2.7 43.5 + - - -
347A LYS 4.2 1.8 + - - -
348A ALA* 2.8 28.8 + - - +
350A ASP* 4.1 12.1 + - - -
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 3.6 14.6 - - + +
98A PHE* 3.8 29.6 - - + -
105A PHE* 5.5 0.2 - - + -
132A ILE* 4.5 2.7 - - + -
133A LYS* 1.3 74.2 - - - +
135A ILE* 1.3 65.0 + - - +
136A SER* 3.5 5.0 + - - +
144A ALA* 4.9 0.4 - - + -
148A HIS* 3.7 27.4 - - + +
154A VAL* 3.5 26.0 - - + -
156A GLU 2.8 9.1 + - - -
157A PHE* 3.3 25.1 - - + -
158A GLU 3.0 25.3 + - - -
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Residues in contact with ILE 135 (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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95A TYR* 4.2 11.0 - - + -
96A TYR 2.8 14.6 + - - +
97A LEU* 3.8 21.3 - - + -
98A PHE 2.9 23.1 + - - -
133A LYS* 4.4 14.4 - - + +
134A VAL* 1.3 72.9 - - - +
136A SER* 1.3 60.6 + - - +
158A GLU 3.3 6.1 - - - +
160A PHE* 3.7 31.4 - - + -
162A ILE* 3.6 17.5 - - + +
345A PHE* 4.9 2.9 - - + -
348A ALA* 4.0 25.6 - - + +
349A ILE* 3.9 25.8 - - + -
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Residues in contact with SER 136 (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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98A PHE* 3.9 12.8 - - - -
134A VAL* 3.5 4.8 + - - -
135A ILE* 1.3 72.4 - - - +
137A GLN* 1.3 60.9 + - - +
138A GLY* 2.6 31.6 + - - -
140A ASN 4.7 0.9 + - - -
141A LEU* 3.8 20.4 - - - -
144A ALA* 3.8 22.7 - - - +
157A PHE* 5.8 0.2 - - - -
158A GLU 2.8 8.5 + - - -
159A TYR* 3.3 3.8 - - - -
160A PHE 2.9 28.0 + - - -
265A PHE* 4.8 2.3 - - - -
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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