Contacts of the helix formed by residues 140 - 152 (chain C) in PDB entry 4IRQ
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 ASN 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C GLN* 2.8 9.5 + - - -
138C ARG 3.2 0.2 + - - -
139C PHE* 1.3 72.5 - - - +
141C ARG* 1.3 62.9 + - - +
142C ALA* 3.7 5.7 + - - +
143C ALA* 3.1 26.1 + - - +
144C LEU* 3.2 25.2 + - - +
219C ASN 3.1 26.4 + - - +
221C PHE 2.8 24.9 + - - +
222C TRP* 3.3 33.8 - - + -
314C LEU* 3.7 16.4 - - + -
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Residues in contact with ARG 141 (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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100C PRO* 3.6 26.9 - - + +
139C PHE* 3.8 22.6 + - + -
140C ASN* 1.3 73.4 + - - +
142C ALA* 1.3 62.5 + - - +
144C LEU* 3.3 4.4 + - - +
145C ILE* 3.1 28.4 + - + +
161C MET* 4.0 36.7 - - - +
163C ASP* 2.9 31.8 + - - -
200C VAL 4.9 0.6 + - - -
201C GLY* 3.9 10.3 - - - -
202C GLY 3.8 26.0 + - - +
204C LEU* 6.1 0.2 - - - +
217C MET* 4.9 3.2 - - - +
221C PHE 4.7 1.0 + - - -
223C GLY 5.9 0.2 + - - -
227C GLU* 3.0 33.5 + - - +
228C ASP* 4.5 4.9 - - - +
402C UDP 3.9 7.0 - - - -
403C TRS 3.7 18.2 + - - +
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Residues in contact with ALA 142 (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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140C ASN* 3.3 4.7 + - - +
141C ARG* 1.3 76.4 - - - +
143C ALA* 1.3 64.8 + - - +
145C ILE* 3.2 4.2 + - - +
146C ASN* 3.1 23.7 + - - -
217C MET* 3.6 29.2 - - + +
218C SER 3.3 21.1 - - - +
221C PHE* 5.4 0.9 - - + -
227C GLU* 3.8 30.1 - - + +
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Residues in contact with ALA 143 (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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140C ASN* 3.1 32.3 + - - +
142C ALA* 1.3 76.0 - - - +
144C LEU* 1.3 57.7 + - - +
146C ASN* 3.1 5.8 + - - +
147C VAL* 2.9 32.5 + - - +
218C SER 4.0 1.2 + - - -
219C ASN* 3.7 27.4 - - + +
222C TRP* 5.7 0.4 - - + -
290C VAL* 4.2 4.6 - - + +
314C LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 144 (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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100C PRO* 4.4 6.1 - - + -
101C PHE 4.2 1.8 - - - +
131C LEU* 3.2 36.5 - - + +
133C GLN* 3.6 23.3 - - + +
139C PHE* 3.6 37.0 - - + -
140C ASN 3.2 16.1 + - - +
141C ARG 3.3 6.7 - - - +
143C ALA* 1.3 77.7 - - - +
145C ILE* 1.3 57.6 + - - +
147C VAL* 3.3 5.5 + - - +
148C GLY 2.9 23.2 + - - -
312C ILE* 3.9 37.0 - - + -
314C LEU* 4.2 7.2 - - + -
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.9 23.8 - - + +
100C PRO* 3.9 30.7 - - + -
131C LEU* 4.3 7.4 - - + -
141C ARG* 3.1 22.1 + - + +
142C ALA 3.2 6.9 + - - +
144C LEU* 1.3 72.8 - - - +
146C ASN* 1.3 60.0 + - - +
148C GLY* 3.3 1.0 + - - -
149C PHE* 2.9 28.1 + - - +
159C ILE* 4.8 0.4 - - + -
161C MET* 3.6 40.4 - - + -
211C TYR* 3.5 20.2 - - + +
217C MET* 3.9 11.2 - - - -
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Residues in contact with ASN 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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142C ALA 3.1 11.2 + - - -
143C ALA 3.1 9.5 + - - +
145C ILE* 1.3 76.5 - - - +
147C VAL* 1.3 62.7 + - - +
149C PHE* 3.1 5.2 + - - +
150C LEU* 3.0 27.4 + - - +
211C TYR* 2.7 28.3 + - - -
216C GLY* 3.6 4.0 - - - -
217C MET 2.7 40.5 + - - -
219C ASN* 2.7 22.2 + - - +
286C GLY 3.7 6.9 - - - -
287C LEU* 3.8 17.6 - - + +
290C VAL* 4.2 10.3 - - + -
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Residues in contact with VAL 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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143C ALA 2.9 18.5 + - - +
144C LEU* 3.6 7.6 - - - +
146C ASN* 1.3 74.8 - - - +
148C GLY* 1.3 56.6 + - - +
150C LEU* 3.1 5.5 + - - +
151C GLU* 2.8 41.8 + - + +
290C VAL* 4.0 5.6 - - + -
292C TYR* 3.6 51.8 - - + -
294C VAL* 4.9 0.2 - - + -
310C LEU* 5.3 0.2 - - + -
312C ILE* 3.6 29.4 - - + -
314C LEU* 3.9 18.8 - - + -
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Residues in contact with GLY 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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98C LEU* 3.6 13.7 - - - +
129C TYR* 5.6 0.6 - - - -
131C LEU* 3.7 26.4 - - - +
144C LEU 2.9 12.6 + - - -
145C ILE 3.3 3.1 + - - -
147C VAL* 1.3 73.4 - - - +
149C PHE* 1.3 66.0 + - - +
151C GLU* 4.4 3.6 - - - -
152C SER* 3.0 29.3 + - - -
310C LEU* 5.0 1.3 - - - +
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Residues in contact with PHE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.8 6.0 - - + +
145C ILE 2.9 13.6 + - - +
146C ASN 3.4 9.2 - - - +
148C GLY* 1.3 77.0 - - - +
150C LEU* 1.3 60.6 + - - +
152C SER* 3.1 19.8 + - - +
159C ILE* 3.9 22.9 - - + -
208C LYS* 3.6 62.2 + - + -
211C TYR* 3.3 43.3 - + + -
212C ARG* 3.6 34.5 + - + -
287C LEU* 3.9 18.4 - - + -
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Residues in contact with LEU 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 ASN 3.0 15.4 + - - +
147C VAL 3.6 5.8 - - - +
149C PHE* 1.3 77.2 - - - +
151C GLU* 1.3 62.3 + - - +
152C SER 3.6 5.0 + - - +
212C ARG* 3.9 25.8 - - - +
287C LEU* 3.7 28.9 - - + +
290C VAL* 3.7 30.5 - - + -
292C TYR* 3.6 24.7 - - + +
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Residues in contact with GLU 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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129C TYR* 4.5 5.1 - - - -
147C VAL* 2.8 35.3 + - + +
148C GLY 3.8 0.9 - - - +
150C LEU* 1.3 72.0 - - - +
152C SER* 1.3 64.5 + - - +
153C SER 4.0 0.2 + - - -
292C TYR* 2.3 38.5 + - + +
294C VAL* 3.7 11.3 - - + +
297C ARG* 2.2 51.6 + - - +
310C LEU* 3.7 21.8 - - + -
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Residues in contact with SER 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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96C ALA* 4.2 8.2 - - - +
98C LEU* 4.5 1.2 - - - +
129C TYR* 3.9 25.6 - - - -
148C GLY 3.0 14.6 + - - -
149C PHE* 3.1 19.1 + - - +
150C LEU 3.4 6.1 - - - +
151C GLU* 1.3 82.4 - - - +
153C SER* 1.3 67.5 + - - +
154C ASN* 3.5 5.4 + - - +
156C THR* 3.7 20.4 + - - +
159C ILE* 5.0 1.7 - - - +
208C LYS* 4.4 6.4 + - - -
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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