Contacts of the helix formed by residues 145 - 154 (chain C) in PDB entry 2JIF
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 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C ILE* 3.0 28.6 + - + +
144C THR* 1.3 91.0 + - - +
146C ILE* 1.3 66.4 + - - +
149C LEU* 3.2 32.4 + - - +
174C PHE* 3.9 43.1 - - + -
289C SER* 3.5 39.5 - - - +
290C LEU* 4.2 10.3 - - + +
293C GLY* 4.3 0.4 - - - -
414C GLU* 4.0 22.4 - - - +
1433C FAD 5.8 1.8 - - + +
1434C COS 5.2 4.0 - - - -
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Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ILE* 3.0 16.9 + - + +
142C GLN* 3.5 11.7 - - - +
145C LEU* 1.3 75.5 - - - +
147C ASN* 1.3 65.9 + - - +
149C LEU* 3.3 2.1 + - - +
150C ILE* 3.2 29.7 + - + +
166C LEU* 3.9 35.0 - - + -
172C GLY* 3.8 21.3 - - - +
173C SER 3.5 35.7 - - - +
174C PHE* 3.7 12.1 - - + +
216C LEU* 4.6 5.4 - - + -
218C LEU* 4.1 18.6 - - + +
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Residues in contact with ASN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C MET 2.7 28.9 + - - +
104C GLY* 3.6 4.0 - - - -
107C VAL* 3.5 31.5 - - + +
142C GLN* 2.8 27.5 + - - +
143C ASN* 3.5 13.5 + - - +
146C ILE* 1.3 73.6 - - - +
148C THR* 1.3 57.5 + - - +
150C ILE* 3.3 2.5 + - - +
151C ARG* 2.8 36.7 + - - +
163C LEU* 4.3 7.2 - - - +
166C LEU* 3.6 29.7 + - - +
167C THR* 5.0 0.8 - - - +
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Residues in contact with THR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU* 4.8 6.1 + - - -
143C ASN 3.0 16.0 + - - -
144C THR 3.5 16.0 + - - +
145C LEU 3.7 0.2 + - - -
146C ILE 3.3 0.8 - - - -
147C ASN* 1.3 77.8 - - - +
149C LEU* 1.3 58.4 + - + +
151C ARG* 3.4 12.7 + - - +
152C LYS* 2.9 57.7 + - + +
289C SER* 5.6 7.2 - - - -
292C GLU* 3.3 32.5 + - - +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU 3.2 21.3 + - - +
146C ILE 3.7 3.1 - - - +
148C THR* 1.3 76.4 - - + +
150C ILE* 1.3 59.9 + - - +
153C HIS* 2.9 48.8 + - + +
154C GLY 3.9 0.3 + - - -
174C PHE* 3.9 13.5 - - + -
218C LEU* 3.4 40.2 - - + -
220C MET* 5.8 0.4 - - - -
234C SER* 5.6 0.2 - - - +
276C LEU* 4.0 9.5 - - + +
285C TYR* 3.5 41.7 - - + +
286C ALA 5.4 0.2 - - - +
289C SER* 3.9 22.2 - - - +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ILE* 3.2 18.4 + - + +
147C ASN 3.9 2.9 - - - +
149C LEU* 1.3 76.3 - - - +
151C ARG* 1.3 59.8 + - - +
154C GLY* 2.9 30.1 + - - +
158C GLN* 4.5 9.9 - - + +
159C LYS* 3.5 20.2 - - + +
162C TYR* 4.3 7.2 - - + -
163C LEU* 3.9 23.8 - - + -
166C LEU* 3.4 30.3 - - + -
216C LEU* 3.9 18.2 - - + -
218C LEU* 4.8 3.1 - - + -
236C LEU* 4.3 20.4 - - + -
276C LEU* 4.4 9.6 - - + -
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Residues in contact with ARG 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU* 3.4 38.9 + - - +
107C VAL* 4.1 17.9 - - - +
108C ASP* 5.3 0.4 - - - +
147C ASN* 2.8 32.8 + - - +
148C THR* 3.7 11.0 + - - +
150C ILE* 1.3 72.8 - - - +
152C LYS* 1.3 92.6 + - + +
159C LYS* 3.2 32.2 + - - -
163C LEU* 4.2 11.7 - - + -
1436C CL 3.2 31.0 - - + +
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Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR* 2.9 35.7 + - + +
151C ARG* 1.3 114.4 - - - +
153C HIS* 1.3 86.7 + - + +
154C GLY 3.8 0.6 - - - +
159C LYS* 5.5 0.4 + - - -
292C GLU* 5.9 1.3 - - - -
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Residues in contact with HIS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C LEU* 2.9 29.1 + - + +
152C LYS* 1.3 95.5 + - + +
154C GLY* 1.3 66.7 + - - +
155C THR* 3.8 2.6 + - - +
158C GLN* 4.5 0.5 - - - +
276C LEU* 3.9 14.8 - - + -
277C GLY* 3.7 27.2 + - - -
285C TYR* 3.2 51.0 + + + +
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Residues in contact with GLY 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ILE* 2.9 21.5 + - - -
152C LYS 3.8 0.9 - - - +
153C HIS* 1.3 80.0 + - - +
155C THR* 1.3 67.7 + - - -
158C GLN* 3.5 14.4 - - - -
159C LYS* 3.5 18.3 + - - -
276C LEU* 3.7 10.2 - - - +
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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