Contacts of the helix formed by residues 296 - 308 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN* 5.1 1.8 + - - -
294A ALA 3.9 2.4 + - - -
295A LEU* 1.3 78.0 - - - +
297A PRO* 1.3 80.0 - - - +
298A ASN* 3.2 38.1 + - - +
299A ALA* 2.9 17.3 + - + +
300A ALA* 3.0 10.4 + - - +
268C ASP 5.4 1.4 + - - -
269C VAL* 4.4 13.3 - - - +
270C LEU 5.2 2.8 + - - +
296C ASN* 4.0 25.8 - - + +
298C ASN* 4.4 2.1 - - - +
299C ALA* 3.8 25.3 - - + +
302C LEU* 5.9 1.2 - - - +
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Residues in contact with PRO 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.1 10.0 - - + +
82A VAL 3.3 14.4 - - - +
83A ASN* 4.4 9.0 - - - +
84A THR 5.3 2.5 - - - +
113A ASN* 3.1 28.3 - - + +
115A THR* 3.3 28.4 + - + -
116A THR* 4.4 2.2 - - - +
295A LEU 3.6 4.7 - - - +
296A ASN* 1.3 99.2 - - - +
298A ASN* 1.3 60.8 + - - +
300A ALA* 3.1 8.0 + - + +
301A TYR* 3.0 22.9 + - - +
268C ASP 6.1 0.7 - - - +
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.8 17.5 - - - +
83A ASN* 3.2 29.7 + - - +
296A ASN* 3.2 19.0 + - - +
297A PRO* 1.3 78.6 - - - +
299A ALA* 1.3 63.1 + - - +
301A TYR* 3.3 6.5 + - - +
302A LEU* 3.1 25.4 + - - +
298B ASN* 5.4 2.9 - - - +
296C ASN* 4.6 0.4 - - - +
298C ASN* 3.7 36.1 + - + +
302C LEU* 4.7 9.3 - - - +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 3.4 27.1 - - + +
270A LEU 4.6 1.1 - - - +
295A LEU* 3.9 16.8 - - + -
296A ASN* 2.9 15.5 + - + +
298A ASN* 1.3 78.4 - - - +
300A ALA* 1.3 65.7 + - - +
302A LEU* 2.9 18.4 + - - +
303A ILE* 3.1 17.4 + - - +
296C ASN* 3.9 19.4 + - + +
298C ASN* 5.8 0.2 - - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR 3.8 14.8 - - - +
116A THR* 3.7 20.4 - - - +
119A LEU* 3.8 9.8 - - + +
295A LEU* 3.6 25.7 - - + +
296A ASN 3.0 7.4 + - - +
297A PRO* 3.1 10.7 + - + +
299A ALA* 1.3 77.4 - - - +
301A TYR* 1.3 56.7 + - - +
303A ILE* 3.4 3.7 + - - +
304A ILE* 3.1 32.1 + - - +
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Residues in contact with TYR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A THR* 4.2 13.4 - - - +
79A THR* 3.6 34.8 - - - -
81A VAL* 4.0 22.9 - - + -
115A THR* 4.5 4.7 + - - +
297A PRO 3.0 11.2 + - - +
298A ASN* 3.7 7.9 - - - +
300A ALA* 1.3 72.3 - - - +
302A LEU* 1.3 70.3 + - + +
303A ILE 3.0 1.8 - - - -
304A ILE* 3.6 15.2 - - + +
305A ARG* 2.8 47.5 + - + +
83B ASN* 3.9 19.2 + - + -
268D ASP* 2.6 43.5 + - - +
302D LEU* 4.8 9.0 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLY 4.9 0.2 - - - +
268A ASP* 3.9 31.6 - - - +
269A VAL* 4.1 12.8 - - + -
298A ASN 3.1 16.9 + - - +
299A ALA* 2.9 10.9 + - - +
301A TYR* 1.3 86.2 - - + +
303A ILE* 1.3 58.4 + - - +
305A ARG* 4.5 2.7 - - - -
306A GLY* 3.2 6.4 + - - -
83C ASN* 4.2 17.3 - - - +
296C ASN* 5.8 1.1 - - - +
298C ASN* 4.7 8.5 - - - +
301D TYR* 5.0 8.5 - - + -
302D LEU* 5.1 10.3 - - + -
305D ARG* 2.9 56.1 + - - +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.4 33.9 - - + -
123A ILE* 5.3 1.1 - - + -
134A LEU* 4.7 0.7 - - + -
259A ALA* 3.9 14.6 - - + -
263A LEU* 4.3 11.4 - - + +
264A GLY* 4.5 8.5 - - - -
269A VAL* 4.0 20.2 - - + -
271A ALA* 3.3 34.5 - - + -
295A LEU* 4.8 1.3 - - + -
299A ALA 3.1 17.1 + - - +
300A ALA* 3.7 6.1 - - - +
301A TYR 3.0 0.6 - - - -
302A LEU* 1.3 77.2 - - - +
304A ILE* 1.3 66.8 + - - +
305A ARG 3.1 1.6 - - - -
306A GLY* 3.6 0.7 - - - +
307A MET* 2.8 33.9 + - + +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU* 3.6 30.7 - - - +
79A THR* 4.6 11.4 - - + +
115A THR* 3.5 26.7 - - - +
118A VAL* 4.0 17.0 - - + -
119A LEU* 3.7 28.0 - - + +
122A LYS* 4.3 8.5 + - + +
300A ALA 3.1 19.1 + - - +
301A TYR* 3.1 17.7 + - + +
303A ILE* 1.3 77.3 - - - +
305A ARG* 1.3 64.5 + - - +
307A MET* 3.3 11.3 + - - +
308A LYS* 3.4 17.6 + - - +
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 2.8 33.2 + - + +
302A LEU* 3.9 7.2 - - - +
304A ILE* 1.3 79.0 - - - +
306A GLY* 1.3 63.2 + - - +
308A LYS* 3.1 26.3 + - + +
309A THR 4.3 0.2 + - - -
264D GLY 3.9 7.5 + - - -
266D HIS* 3.4 46.8 + - + +
268D ASP* 2.5 45.8 + - - +
269D VAL* 4.2 4.0 - - - +
302D LEU* 2.8 47.2 + - - +
305D ARG* 3.9 21.4 - - - +
306D GLY* 3.5 15.0 - - - +
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Residues in contact with GLY 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU 3.9 2.5 - - - -
264A GLY 3.7 13.7 - - - -
266A HIS* 4.0 8.5 - - - -
302A LEU 3.2 6.4 + - - -
303A ILE 3.1 5.9 + - - -
305A ARG* 1.3 80.6 - - - +
307A MET* 1.3 60.3 + - - +
309A THR* 3.4 13.2 + - - -
313A ARG* 2.9 24.2 + - - -
305D ARG* 3.4 15.5 - - - +
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Residues in contact with MET 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 3.5 21.4 - - + +
119A LEU* 3.6 29.6 - - - -
122A LYS* 3.9 23.3 - - + -
123A ILE* 4.0 17.5 - - + +
126A LEU* 3.5 31.2 - - + -
263A LEU* 3.4 33.4 - - + +
303A ILE* 2.8 16.6 + - + +
304A ILE* 3.7 6.5 - - - +
305A ARG 3.1 0.4 - - - -
306A GLY* 1.3 72.3 - - - +
308A LYS* 1.3 61.7 + - - +
309A THR 2.9 7.7 + - - -
310A LEU* 2.9 25.1 + - + +
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 4.2 5.8 - - - -
62A ILE* 3.0 60.2 + - + +
63A HIS* 5.8 0.6 - - - -
66A GLU* 3.0 23.7 + - - +
77A ILE 5.3 2.4 + - - -
78A THR* 5.8 1.6 - - - +
122A LYS* 3.2 14.6 - - - +
304A ILE* 3.4 12.3 - - - +
305A ARG* 3.1 22.6 + - + +
307A MET* 1.3 78.1 - - - +
309A THR* 1.3 60.2 + - - +
310A LEU 3.6 0.2 - - - -
311A HIS* 3.5 8.0 - - - -
266D HIS* 4.0 8.7 - - + +
392D CYS* 4.0 18.5 - - + -
393D GLU* 2.8 35.2 + - - +
428D VAL* 3.8 3.1 - - - +
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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