Contacts of the strand formed by residues 124 - 131 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 4.6 22.2 - - + -
112B VAL* 5.1 13.9 - - + -
114B ASP 4.0 9.6 - - - +
115B VAL* 4.5 12.1 - - + -
122B VAL* 4.9 10.1 - - + -
123B VAL* 1.3 79.8 - - - +
125B ILE* 1.3 63.0 + - - +
126B MET* 5.0 5.8 - - + +
142B PHE 3.5 2.8 - - - +
144B LEU* 2.9 64.5 + - + +
145B PHE 6.3 0.9 - - - -
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU* 5.5 0.4 - - - +
112B VAL* 4.0 1.7 - - - +
113B ALA* 3.0 30.6 + - + -
114B ASP* 3.3 23.6 + - + +
115B VAL* 4.8 0.6 - - - +
123B VAL* 4.1 8.6 + - + -
124B ILE* 1.3 74.3 - - - +
126B MET* 1.3 62.2 + - - +
141B GLN* 3.2 38.1 - - + +
142B PHE 3.5 3.4 - - - -
143B SER* 4.3 20.9 - - - +
160B LYS 4.1 5.4 - - - +
161B VAL* 3.2 50.0 - - + -
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Residues in contact with MET 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 3.3 30.1 - - - -
65B GLY 5.9 0.2 - - - +
68B SER* 3.9 28.5 - - - +
110B ALA* 4.1 11.0 - - + -
111B VAL 3.4 20.2 - - - +
112B VAL* 3.9 9.6 - - + -
124B ILE* 3.8 4.7 + - + +
125B ILE* 1.3 75.0 - - - +
127B ASP* 1.3 68.3 + - - +
128B VAL* 4.0 4.0 - - + +
140B ASN 3.6 1.9 - - - +
141B GLN* 4.4 1.1 - - - -
142B PHE* 3.0 53.5 + - + +
144B LEU* 4.6 22.9 - - + -
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Residues in contact with ASP 127 (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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111B VAL* 2.8 38.3 + - + +
113B ALA* 3.1 23.5 - - + +
125B ILE 4.2 0.4 - - - -
126B MET* 1.3 75.5 - - - +
128B VAL* 1.3 60.1 - - - +
129B TYR* 3.7 24.6 + - + +
139B HIS* 2.4 32.3 + - - +
140B ASN 3.3 2.5 - - - -
141B GLN* 3.0 27.9 + - - +
160B LYS* 4.5 2.6 - - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.4 13.7 - - + -
65B GLY* 3.9 25.6 - - - +
108B CYS* 4.6 0.7 - - + -
109B GLU 3.3 12.8 - - - +
110B ALA* 4.1 10.5 - - + -
126B MET* 4.0 5.2 - - + +
127B ASP* 1.3 77.9 - - - +
129B TYR* 1.3 71.4 + - - +
130B SER* 4.2 2.6 + - - +
138B CYS 4.0 0.7 - - - +
139B HIS* 3.5 2.7 - - - -
140B ASN* 2.8 50.1 + - + +
142B PHE* 3.4 32.8 - - + -
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Residues in contact with TYR 129 (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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97B TYR* 5.0 3.4 - - - -
108B CYS* 3.2 2.4 - - - +
109B GLU* 2.7 44.7 + - + +
111B VAL* 5.1 13.2 - - + -
127B ASP* 3.7 34.3 + - + +
128B VAL* 1.3 74.6 - - - +
130B SER* 1.3 61.9 + - - +
131B TYR* 3.5 31.3 - - + +
136B LEU* 3.7 23.8 - - + -
138B CYS 3.6 2.7 - - - -
139B HIS* 3.8 34.7 + + + -
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Residues in contact with SER 130 (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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64B ILE* 3.5 15.6 - - - +
65B GLY* 4.4 7.8 - - - -
106B LEU* 4.7 7.0 - - - -
107B LYS 3.3 4.3 - - - -
108B CYS* 3.3 25.2 - - - +
128B VAL* 4.4 3.3 + - - +
129B TYR* 1.3 75.6 - - - +
131B TYR* 1.3 62.5 + - - +
136B LEU* 3.6 1.3 - - - +
137B ILE* 2.8 27.6 + - - +
138B CYS* 3.0 32.8 + - - -
140B ASN* 4.8 0.5 + - - -
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Residues in contact with TYR 131 (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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106B LEU* 3.1 10.0 - - - +
107B LYS* 2.6 59.5 + - + +
109B GLU* 3.6 36.7 + - - -
129B TYR* 3.5 38.1 - - + +
130B SER* 1.3 74.5 - - - +
132B SER* 1.3 61.6 + - - +
133B GLU 5.0 7.2 - - - +
136B LEU* 3.5 42.1 - - + +
137B ILE* 4.3 0.4 - - - +
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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