Contacts of the strand formed by residues 124 - 131 (chain J) in PDB entry 1S9C
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 124 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J ILE* 3.2 40.6 - - + -
84J PHE* 5.3 2.2 - - + -
87J VAL* 5.4 0.7 - - + -
112J VAL* 3.9 25.4 - - + -
114J ASP 3.6 4.7 - - - +
115J VAL* 4.3 10.3 - - + +
122J VAL* 3.5 15.7 - - + +
123J VAL* 1.3 74.6 - - - +
125J ILE* 1.3 59.8 - - - +
126J MET* 3.4 8.3 + - + +
142J PHE 4.1 0.3 - - - +
144J LEU* 3.1 46.5 + - + +
145J PHE* 4.3 2.2 - - - +
146J LEU* 4.7 14.1 - - + -
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Residues in contact with ILE 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J VAL* 3.5 4.5 - - - +
113J ALA* 3.4 24.3 + - + -
114J ASP* 2.9 36.2 + - + +
116J LEU* 4.3 13.5 - - + -
123J VAL* 3.2 30.1 - - + -
124J ILE* 1.3 68.7 - - - +
126J MET* 1.3 61.2 + - - +
141J GLN* 3.8 29.4 - - + +
142J PHE 3.8 4.9 - - - -
143J SER* 4.4 11.9 - - - +
160J LYS 4.4 1.6 - - - +
161J VAL* 3.2 34.5 - - + -
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Residues in contact with MET 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J LEU* 3.9 26.0 - - - -
65J GLY 5.7 1.3 - - - +
68J SER* 4.6 10.5 - - - +
69J MET* 3.7 30.3 - - - -
84J PHE* 3.9 21.8 - - + -
110J ALA* 4.5 5.6 - - + -
111J VAL 3.4 14.6 - - - +
112J VAL* 4.9 4.7 - - + -
124J ILE* 3.4 10.3 + - + +
125J ILE* 1.3 74.1 - - - +
127J ASP* 1.3 72.2 + - - +
128J VAL* 5.0 4.9 - - + -
140J ASN 3.7 0.3 - - - +
141J GLN* 3.4 1.6 - - - -
142J PHE* 2.9 61.0 + - + +
144J LEU* 4.5 7.9 - - + -
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Residues in contact with ASP 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ALA* 3.3 3.6 - - - +
111J VAL* 3.0 35.7 + - + +
113J ALA* 3.2 26.0 - - + +
125J ILE 4.3 0.8 + - - -
126J MET* 1.3 72.7 - - - +
128J VAL* 1.3 61.6 + - - +
129J TYR* 3.7 23.6 + - + -
139J HIS* 2.6 30.8 + - - +
140J ASN 3.2 2.2 - - - -
141J GLN* 2.7 35.3 + - - +
160J LYS 4.3 2.3 - - - +
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Residues in contact with VAL 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J PHE* 4.5 6.5 - - + -
65J GLY* 4.0 24.9 - - - +
68J SER* 5.4 1.3 - - - +
108J CYS* 4.4 11.4 - - + -
109J GLU 3.3 16.2 - - - +
110J ALA* 4.1 8.3 - - + -
126J MET* 4.5 6.3 - - + +
127J ASP* 1.3 78.8 - - - +
129J TYR* 1.3 69.4 + - - +
130J SER* 4.1 1.7 + - - +
138J CYS 4.0 0.9 - - - +
139J HIS* 3.7 1.4 - - - -
140J ASN* 2.9 39.4 + - + +
142J PHE* 3.4 35.7 - - + -
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Residues in contact with TYR 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J TYR* 4.9 4.7 - - - -
108J CYS* 3.3 1.4 - - - -
109J GLU* 2.8 38.7 + - + +
110J ALA 6.1 0.4 - - - -
111J VAL* 5.7 7.0 - - + -
127J ASP* 3.7 28.3 + - + +
128J VAL* 1.3 74.5 - - - +
130J SER* 1.3 61.1 + - - +
131J TYR* 3.5 34.7 - - + +
136J LEU* 3.7 19.1 - - + -
138J CYS 3.6 2.7 - - - -
139J HIS* 3.6 45.5 + + + -
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Residues in contact with SER 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J ILE* 3.6 14.2 - - - +
65J GLY* 4.6 2.9 - - - -
106J LEU* 4.7 7.4 - - - -
107J LYS 3.3 5.2 - - - -
108J CYS* 3.2 27.4 - - - +
128J VAL* 4.5 7.3 + - - +
129J TYR* 1.3 75.4 - - - +
131J TYR* 1.3 62.0 + - - +
136J LEU* 3.7 1.4 - - - +
137J ILE* 2.9 27.4 + - - +
138J CYS* 3.1 31.6 + - - -
140J ASN* 4.9 0.3 + - - -
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Residues in contact with TYR 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J LEU* 3.4 7.1 - - - -
107J LYS* 2.7 52.7 + - + +
109J GLU* 3.6 33.5 + - - -
129J TYR* 3.5 39.0 - - + +
130J SER* 1.3 75.2 - - - +
132J SER* 1.3 62.7 + - - +
133J GLU* 4.4 3.6 - - - +
135J GLU 3.4 14.8 - - - +
136J LEU* 3.5 36.6 - - + +
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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