Contacts of the helix formed by residues 155 - 167 (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 THR 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153C HIS 5.3 1.8 - - - +
154C GLY* 1.3 75.8 - - - -
156C GLU* 1.3 64.1 + - - +
157C GLU* 3.6 25.5 + - - +
158C GLN* 3.0 39.4 + - - +
159C LYS* 2.9 23.7 + - - +
275C ILE 6.0 0.2 - - - +
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Residues in contact with GLU 156 (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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111C TYR* 4.5 9.5 + - - -
155C THR* 1.3 73.8 - - - +
157C GLU* 1.3 66.1 + - + +
159C LYS* 3.6 24.7 + - - +
160C ALA* 2.9 31.9 + - - +
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Residues in contact with GLU 157 (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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155C THR* 3.6 19.5 + - - +
156C GLU* 1.3 89.6 + - + +
158C GLN* 1.3 56.1 + - + +
160C ALA* 3.4 6.0 + - - +
161C THR* 2.7 38.2 + - - +
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Residues in contact with GLN 158 (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* 4.5 4.4 - - + +
153C HIS 4.5 1.2 - - - +
154C GLY* 3.5 11.6 - - - -
155C THR* 3.0 43.0 + - - +
157C GLU* 1.3 73.2 - - + +
159C LYS* 1.3 60.9 + - - +
161C THR* 3.3 3.0 + - - -
162C TYR* 2.8 42.0 + - + +
236C LEU* 3.9 29.9 - - + +
273C ALA 2.8 28.9 + - - +
274C ASN* 3.9 1.4 - - - +
275C ILE 3.0 21.5 + - - +
276C LEU* 3.9 5.9 - - - +
277C GLY 4.9 0.5 + - - -
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Residues in contact with LYS 159 (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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111C TYR* 3.6 23.4 - - + +
150C ILE* 3.5 26.0 - - + +
151C ARG* 3.2 23.0 + - - +
152C LYS 5.5 0.6 - - - -
154C GLY 3.5 18.3 + - - +
155C THR 2.9 16.3 + - - +
156C GLU* 3.6 26.2 + - - +
158C GLN* 1.3 75.3 - - - +
160C ALA* 1.3 62.6 + - - +
163C LEU* 3.1 46.1 + - + +
164C PRO* 3.2 6.2 - - - +
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Residues in contact with ALA 160 (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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111C TYR* 3.8 15.0 - - + -
156C GLU 2.9 20.3 + - - +
157C GLU* 3.7 6.3 - - - +
159C LYS* 1.3 77.1 - - - +
161C THR* 1.3 60.9 + - - +
164C PRO* 3.3 17.9 - - - +
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Residues in contact with THR 161 (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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157C GLU* 2.7 21.7 + - - +
158C GLN* 3.7 5.2 - - - -
159C LYS 3.2 0.2 - - - -
160C ALA* 1.3 80.5 - - - +
162C TYR* 1.3 86.6 + - + +
163C LEU 3.7 0.2 - - - -
164C PRO* 4.0 4.0 - - - +
165C GLN* 3.6 27.4 + - - +
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Residues in contact with TYR 162 (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* 4.3 9.4 - - + -
158C GLN* 2.8 34.2 + - + +
161C THR* 1.3 91.3 - - + +
163C LEU* 1.3 59.4 + - - +
165C GLN* 3.0 23.4 + - - +
166C LEU* 2.8 43.9 + - + +
170C LYS* 4.6 7.0 - - + -
216C LEU* 3.8 32.1 - - + -
236C LEU* 3.8 31.3 - - + +
238C ASP* 3.1 24.6 + - - -
274C ASN* 3.7 20.9 + - - -
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Residues in contact with LEU 163 (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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107C VAL* 4.3 20.2 - - + -
111C TYR* 3.7 35.4 - - + -
147C ASN* 4.3 15.0 - - - +
150C ILE* 3.9 27.4 - - + -
151C ARG* 4.2 4.7 - - + -
159C LYS* 3.1 36.5 + - + +
162C TYR* 1.3 75.0 - - - +
164C PRO* 1.3 61.3 - - + +
166C LEU* 3.2 12.8 + - + -
167C THR* 2.9 35.2 + - - +
1436C CL 4.0 13.0 - - + -
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Residues in contact with PRO 164 (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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110C GLU 5.3 1.1 - - - +
111C TYR* 3.4 32.5 - - + +
159C LYS 3.2 14.1 - - - +
160C ALA* 3.3 20.0 - - - +
161C THR 4.0 2.9 - - - +
162C TYR 3.6 2.0 - - - -
163C LEU* 1.3 90.9 - - + +
165C GLN* 1.3 51.1 + - + +
167C THR* 3.2 9.5 + - - -
168C THR* 2.5 30.9 + - + +
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Residues in contact with GLN 165 (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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161C THR* 3.6 25.6 + - - +
162C TYR* 3.0 21.0 + - - +
164C PRO* 1.3 75.3 - - + +
166C LEU* 1.3 61.3 + - - +
168C THR* 3.5 4.9 - - - -
169C GLU* 2.9 17.6 + - + -
170C LYS* 2.8 72.1 + - + +
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Residues in contact with LEU 166 (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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98C PHE* 3.3 9.5 - - - -
103C MET 3.7 7.9 - - - +
142C GLN* 2.9 27.0 + - - +
146C ILE* 3.9 15.9 - - + -
147C ASN* 3.6 22.0 - - - +
150C ILE* 3.4 33.0 - - + -
162C TYR* 2.8 26.7 + - + +
163C LEU* 3.7 11.4 - - + +
165C GLN* 1.3 77.8 - - + +
167C THR* 1.3 59.1 + - + +
168C THR 3.3 0.2 - - - -
170C LYS* 3.5 26.5 - - + +
172C GLY 4.2 8.3 - - - +
216C LEU* 4.2 13.7 - - + -
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Residues in contact with THR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C PHE* 3.7 21.5 - - - +
101C GLY* 5.5 2.4 - - - -
103C MET* 4.5 9.1 + - - +
104C GLY* 3.9 14.6 + - - -
107C VAL* 3.7 31.9 - - + -
111C TYR 2.7 25.1 + - - +
112C GLY* 3.6 20.6 + - - +
113C GLY* 4.1 3.1 - - - +
147C ASN* 5.0 0.4 - - - +
163C LEU* 2.9 16.0 + - - +
164C PRO 3.2 9.9 + - - -
166C LEU* 1.3 78.6 - - + +
168C THR* 1.3 61.9 + - - +
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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