Contacts of the helix formed by residues 296 - 308 (chain C) in PDB entry 1I43
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 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A ASP 5.3 0.8 + - - -
269A VAL* 4.2 15.0 - - - +
270A LEU 5.1 3.0 + - - +
296A ASN* 4.0 24.3 - - + +
298A ASN* 4.6 1.2 - - - +
299A ALA* 3.9 24.7 - - + +
302A LEU* 5.8 1.0 - - - +
83C ASN* 4.9 4.6 + - - -
294C ALA 4.0 2.2 + - - -
295C LEU* 1.3 76.2 - - - +
297C PRO* 1.3 77.5 - - - +
298C ASN* 3.0 40.1 + - - +
299C ALA* 2.9 17.5 + - + +
300C ALA* 3.0 9.6 + - - +
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Residues in contact with PRO 297 (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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81C VAL* 4.0 11.6 - - + +
82C VAL 3.3 12.8 - - - +
83C ASN* 4.7 7.0 - - - +
84C THR 5.4 2.7 - - - +
113C ASN* 3.1 29.4 - - + +
115C THR* 3.4 27.7 + - + -
116C THR* 4.4 1.8 - - - +
295C LEU 3.6 4.7 - - - +
296C ASN* 1.3 99.0 - - - +
298C ASN* 1.3 60.7 + - - +
300C ALA* 3.1 8.1 + - + +
301C TYR* 3.0 23.7 + - - +
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Residues in contact with ASN 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASN* 4.4 0.4 - - - +
298A ASN* 3.7 36.8 - - + +
302A LEU* 4.7 10.7 - - - +
81C VAL* 3.9 17.8 - - - +
83C ASN* 3.4 27.5 + - - +
296C ASN* 3.0 17.7 + - - +
297C PRO* 1.3 78.7 - - - +
299C ALA* 1.3 59.6 + - - +
301C TYR* 3.6 5.3 + - - +
302C LEU* 3.3 26.1 + - - +
298D ASN* 5.5 3.3 - - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASN* 3.8 20.8 + - + +
269C VAL* 3.5 27.0 - - + +
270C LEU 4.7 0.7 - - - +
295C LEU* 4.2 15.3 - - + -
296C ASN* 2.9 13.6 + - + +
298C ASN* 1.3 79.3 - - - +
300C ALA* 1.3 65.1 + - - +
302C LEU* 3.1 16.9 + - - +
303C ILE* 3.1 18.8 + - - +
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Residues in contact with ALA 300 (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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115C THR 3.8 14.4 - - - +
116C THR* 3.6 26.0 - - - +
119C LEU* 3.9 10.3 - - + +
295C LEU* 3.7 19.9 - - + +
296C ASN 3.0 7.4 + - - +
297C PRO* 3.4 10.3 - - + +
299C ALA* 1.3 77.2 - - - +
301C TYR* 1.3 57.8 + - - +
303C ILE* 3.4 3.7 + - - +
304C ILE* 3.0 32.8 + - - +
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Residues in contact with TYR 301 (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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266B HIS 5.2 0.2 + - - -
268B ASP* 2.8 41.2 + - - +
302B LEU* 5.0 9.0 - - + -
78C THR* 4.2 13.2 - - - +
79C THR* 3.4 34.1 - - - -
81C VAL* 4.0 22.0 - - + -
115C THR* 4.6 4.9 + - - +
297C PRO 3.0 14.1 + - - +
298C ASN* 3.9 5.6 - - - +
300C ALA* 1.3 72.9 - - - +
302C LEU* 1.3 70.6 + - + +
303C ILE 3.0 2.0 + - - -
304C ILE* 3.0 15.5 + - + +
305C ARG* 2.8 49.7 + - + +
83D ASN* 3.8 20.4 + - + -
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Residues in contact with LEU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 4.4 16.6 - - - +
296A ASN* 5.9 1.3 - - - +
298A ASN* 4.7 7.4 - - - +
301B TYR* 4.8 8.7 - - + -
302B LEU* 5.1 10.8 - - + -
305B ARG* 2.6 59.2 + - - +
264C GLY 4.9 0.2 - - - +
268C ASP* 3.9 30.3 - - - +
269C VAL* 4.2 11.2 - - + -
298C ASN 3.3 12.3 + - - +
299C ALA* 3.1 13.7 + - - +
301C TYR* 1.3 86.9 - - + +
303C ILE* 1.3 57.9 + - - +
305C ARG* 4.5 1.8 - - - -
306C GLY* 3.2 6.6 + - - -
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Residues in contact with ILE 303 (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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119C LEU* 3.4 35.4 - - + -
123C ILE* 5.2 1.3 - - + -
134C LEU* 4.7 0.9 - - + -
259C ALA* 3.8 19.3 - - + -
263C LEU* 4.2 6.4 - - + +
264C GLY* 4.5 9.4 - - - -
269C VAL* 4.1 20.6 - - + -
271C ALA* 3.3 33.9 - - + -
295C LEU* 4.9 1.3 - - + -
299C ALA 3.1 15.2 + - - +
300C ALA* 3.7 7.2 - - - +
301C TYR 3.0 0.4 - - - -
302C LEU* 1.3 76.3 - - - +
304C ILE* 1.3 65.0 + - - +
305C ARG 3.1 1.3 - - - -
306C GLY* 3.6 0.2 - - - -
307C MET* 2.8 35.6 + - + +
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Residues in contact with ILE 304 (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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66C GLU* 3.9 28.7 - - - +
79C THR* 4.5 12.1 - - + +
115C THR* 3.5 25.8 - - - +
118C VAL* 3.9 18.8 - - + -
119C LEU* 3.8 26.7 - - + +
122C LYS* 4.2 8.4 + - + +
300C ALA 3.0 23.9 + - - +
301C TYR* 3.0 17.4 + - + +
303C ILE* 1.3 76.4 - - - +
305C ARG* 1.3 63.7 + - - +
307C MET* 3.4 10.0 + - - +
308C LYS* 3.4 20.7 + - - +
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Residues in contact with ARG 305 (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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264B GLY 4.2 6.7 + - - -
266B HIS* 3.5 42.3 + - + +
268B ASP* 2.5 45.6 + - - +
269B VAL* 4.2 3.8 - - - +
302B LEU* 2.7 50.3 + - - +
305B ARG* 3.9 25.9 - - - +
306B GLY* 3.5 19.0 - - - +
301C TYR* 2.8 32.9 + - + +
302C LEU* 4.3 2.5 - - - -
304C ILE* 1.3 78.3 - - - +
306C GLY* 1.3 65.2 + - - +
308C LYS* 3.1 24.8 + - + +
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Residues in contact with GLY 306 (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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305B ARG* 3.5 11.6 - - - +
263C LEU 4.0 1.6 - - - -
264C GLY 3.6 17.9 - - - -
266C HIS* 3.9 8.5 - - - -
302C LEU 3.2 6.8 + - - -
303C ILE 3.1 5.2 + - - -
305C ARG* 1.3 79.5 - - - +
307C MET* 1.3 61.9 + - - +
309C THR* 3.2 15.0 + - - -
313C ARG* 2.8 22.5 + - - -
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Residues in contact with MET 307 (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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61C ALA* 3.5 21.9 - - + +
119C LEU* 3.8 27.8 - - - -
122C LYS* 4.1 17.3 - - + -
123C ILE* 4.0 20.6 - - + -
126C LEU* 3.5 32.5 - - + -
263C LEU* 3.3 29.8 - - + +
303C ILE* 2.8 18.2 + - - +
304C ILE* 3.7 6.5 - - - +
305C ARG 3.2 0.2 - - - -
306C GLY* 1.3 72.0 - - - +
308C LYS* 1.3 61.5 + - - +
309C THR 3.0 5.8 - - - -
310C LEU* 3.0 27.3 + - + +
313C ARG* 4.0 4.9 - - - +
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Residues in contact with LYS 308 (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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266B HIS* 3.9 18.2 - - + +
392B CYS* 4.0 10.3 - - + -
393B GLU* 3.0 35.4 + - - +
428B VAL* 3.9 2.9 - - - +
61C ALA 4.3 1.8 - - - -
62C ILE* 2.8 55.4 + - + +
63C HIS* 5.7 0.8 - - - -
66C GLU* 2.7 28.1 + - - +
77C ILE 5.4 1.6 + - - -
78C THR* 6.0 0.6 - - - +
122C LYS* 3.1 15.7 - - - +
304C ILE* 3.4 13.9 + - - +
305C ARG* 3.1 23.9 + - + +
307C MET* 1.3 78.1 - - - +
309C THR* 1.3 60.4 + - - +
310C LEU 3.5 0.2 - - - -
311C HIS* 3.5 7.8 - - - -
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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