Contacts of the helix formed by residues 118 - 127 (chain B) in PDB entry 1JSC
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 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TYR 4.4 5.6 - - - +
115B GLY 3.5 21.5 - - - +
117B ALA* 1.3 77.9 - - - +
119B LEU* 1.3 65.6 + - - +
120B PRO* 3.3 4.0 - - - -
121B VAL* 3.0 22.3 + - + -
122B TYR* 2.8 29.0 + - + +
160B LEU* 3.5 37.5 - - + -
161B VAL 3.6 13.7 - - - +
162B THR* 3.8 18.3 + - - +
188B THR 4.3 0.7 - - - -
189B GLY* 3.8 22.4 - - - +
249B LEU* 4.1 13.0 - - + -
254B THR* 5.6 0.7 - - + -
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Residues in contact with LEU 119 (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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114B PRO* 5.8 2.0 - - + -
115B GLY 3.1 16.1 + - - +
116B GLY* 3.3 17.0 - - - +
118B ILE* 1.3 76.6 - - - +
120B PRO* 1.3 72.5 - - + +
122B TYR* 4.1 11.7 - - + -
123B ASP* 2.8 60.3 + - - +
251B LYS* 5.2 7.4 - - - +
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Residues in contact with PRO 120 (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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95B GLY* 3.8 7.4 - - - +
116B GLY 4.3 2.2 - - - +
117B ALA 4.0 9.4 - - - +
118B ILE 3.4 4.0 - - - -
119B LEU* 1.3 97.0 - - + +
121B VAL* 1.3 59.2 + - - +
123B ASP* 4.3 4.1 - - + +
124B ALA* 3.6 18.0 + - - +
251B LYS* 4.3 14.8 - - + +
254B THR* 3.3 36.6 - - - +
255B ALA* 3.9 21.1 - - + +
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Residues in contact with VAL 121 (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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95B GLY* 4.3 11.0 - - - -
98B PHE* 3.4 45.3 - - + -
118B ILE* 3.0 22.0 + - + +
120B PRO* 1.3 74.6 - - - +
122B TYR* 1.3 67.4 + - - +
124B ALA* 3.1 3.6 + - - +
125B ILE* 3.0 21.4 + - + +
160B LEU* 3.9 16.8 - - + -
249B LEU* 4.2 6.7 - - + -
254B THR* 3.5 35.0 - - + -
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Residues in contact with TYR 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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596A SER 4.8 2.2 - - - -
598A THR* 2.6 44.2 + - - +
113B TYR 4.5 2.0 - - - -
114B PRO* 3.7 37.0 - - + -
115B GLY 5.6 0.2 - - - +
118B ILE* 2.8 24.2 + - + +
119B LEU* 3.6 13.0 - - + +
121B VAL* 1.3 78.1 - - - +
123B ASP* 1.3 67.1 + - - +
125B ILE* 3.7 0.5 - - - +
126B HIS* 2.7 63.7 + + + +
133B PHE* 3.3 37.0 - + - -
135B LEU* 3.8 5.4 - - - +
160B LEU* 4.0 13.2 - - + +
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Residues in contact with ASP 123 (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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596A SER* 3.0 28.8 + - - +
119B LEU* 2.8 53.8 + - - +
120B PRO* 4.3 4.4 - - + +
122B TYR* 1.3 77.2 - - - +
124B ALA* 1.3 63.3 + - - +
126B HIS* 4.5 0.4 - - - -
127B ASN* 2.8 42.3 + - - +
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Residues in contact with ALA 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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95B GLY* 3.3 35.0 - - - +
96B GLN* 4.3 6.3 - - + +
99B ASN* 2.9 21.4 + - + +
120B PRO 3.6 9.1 + - - +
121B VAL 3.1 9.0 + - - +
123B ASP* 1.3 81.8 - - - +
125B ILE* 1.3 60.0 + - + +
127B ASN* 4.1 1.9 - - - +
128B SER* 3.4 12.6 + - - -
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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
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98B PHE* 3.7 39.3 - - + -
99B ASN* 4.0 7.0 - - - +
102B MET* 4.1 9.4 - - + -
110B VAL* 4.3 15.9 - - + -
121B VAL* 3.0 18.4 + - + +
122B TYR 3.9 1.8 - - - +
124B ALA* 1.3 73.5 - - + +
126B HIS* 1.3 67.2 + - - +
128B SER* 3.2 20.3 + - - +
131B PHE* 3.9 39.4 - - + +
133B PHE* 3.5 30.6 - - + +
160B LEU* 4.5 6.7 - - + -
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Residues in contact with HIS 126 (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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596A SER 3.5 26.7 + - - -
597A HIS 4.0 6.1 - - - -
598A THR* 3.9 13.9 + - + +
122B TYR* 2.7 62.7 + + + +
123B ASP* 4.2 2.5 - - - +
125B ILE* 1.3 75.0 - - - +
127B ASN* 1.3 69.9 + - - +
128B SER 3.7 3.5 + - - +
133B PHE* 4.6 21.9 - + + +
135B LEU* 4.9 5.2 - - + +
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Residues in contact with ASN 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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596A SER* 3.7 30.0 + - - +
123B ASP* 2.8 38.1 + - - +
124B ALA* 4.1 2.9 - - - +
126B HIS* 1.3 82.9 + - - +
128B SER* 1.3 61.6 + - - +
129B ASP 3.8 1.4 + - - -
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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