Contacts of the helix formed by residues 296 - 307 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268J ASP 5.4 0.8 + - - -
269J VAL* 4.2 14.6 - - - +
270J LEU 5.2 2.4 + - - +
296J ASN* 4.0 25.1 - - + +
298J ASN* 4.6 1.6 - - - +
299J ALA* 3.9 24.9 + - + +
302J LEU* 5.8 1.2 - - - +
83L ASN* 5.0 2.6 + - - -
294L ALA 4.0 1.6 + - - -
295L LEU* 1.3 76.9 - - - +
297L PRO* 1.3 72.6 - - - +
298L ASN* 3.1 39.3 + - - +
299L ALA* 3.0 10.6 + - + +
300L ALA* 2.9 25.3 + - - +
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Residues in contact with PRO 297 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268J ASP 6.0 0.7 - - - +
81L VAL* 4.0 11.2 - - + +
82L VAL 3.4 12.6 - - - +
83L ASN* 4.5 8.3 - - - +
84L THR 5.3 2.5 - - - +
113L ASN* 3.1 27.4 - - + +
115L THR* 3.2 31.3 + - + -
116L THR* 4.4 2.2 - - - +
295L LEU 3.7 4.0 - - - +
296L ASN* 1.3 100.2 - - - +
298L ASN* 1.3 59.7 + - - +
300L ALA* 3.5 7.8 - - + +
301L TYR* 3.1 23.0 + - - +
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Residues in contact with ASN 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298J ASN* 4.0 34.0 + - + +
302J LEU* 4.6 10.1 - - - +
298K ASN* 5.5 2.9 - - - +
81L VAL* 3.6 17.7 - - - +
83L ASN* 3.3 28.9 + - - +
296L ASN* 3.1 19.6 + - - +
297L PRO* 1.3 77.7 - - - +
299L ALA* 1.3 60.6 + - - +
301L TYR* 3.5 6.1 + - - +
302L LEU* 3.2 27.5 + - + +
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Residues in contact with ALA 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296J ASN* 3.7 20.1 + - + +
269L VAL* 3.4 26.9 - - + +
270L LEU 4.6 0.9 - - - +
295L LEU* 4.0 16.2 - - + -
296L ASN* 3.0 14.0 + - + +
298L ASN* 1.3 77.8 - - - +
300L ALA* 1.3 65.6 + - - +
302L LEU* 3.0 18.3 + - - +
303L ILE* 3.1 18.2 + - - +
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Residues in contact with ALA 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L THR 3.8 13.5 - - - +
116L THR* 3.8 20.0 - - - +
119L LEU* 3.7 9.5 - - + +
295L LEU* 3.7 25.5 - - + +
296L ASN 2.9 8.3 + - - +
297L PRO* 3.5 9.9 - - + +
298L ASN 3.3 0.2 - - - -
299L ALA* 1.3 77.6 - - - +
301L TYR* 1.3 57.8 + - - +
303L ILE* 3.3 4.7 + - - +
304L ILE* 3.0 31.9 + - - +
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Residues in contact with TYR 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266I HIS 5.1 0.2 + - - -
268I ASP* 2.6 42.3 + - - +
302I LEU* 4.9 9.4 - - + -
83K ASN* 3.9 18.8 + - + -
78L THR* 4.3 7.7 - - - +
79L THR* 3.6 39.9 - - - -
81L VAL* 3.9 20.4 - - + -
115L THR* 4.5 4.2 + - - +
297L PRO 3.1 16.5 + - - +
298L ASN 3.7 5.4 - - - +
300L ALA* 1.3 71.4 - - - +
302L LEU* 1.3 68.8 + - + +
303L ILE 3.0 2.0 - - - -
304L ILE* 3.5 15.7 - - + +
305L ARG* 2.8 49.1 + - + +
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Residues in contact with LEU 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301I TYR* 4.9 8.3 - - + -
302I LEU* 5.2 10.5 - - + -
305I ARG* 2.7 59.3 + - - +
83J ASN* 4.2 17.7 - - + +
296J ASN* 5.7 1.1 - - - +
298J ASN* 4.6 8.1 - - - +
268L ASP* 4.1 17.3 - - - +
269L VAL* 4.1 22.2 - - + -
298L ASN 3.2 18.0 + - - +
299L ALA* 3.0 13.1 + - - +
301L TYR* 1.3 86.0 - - + +
303L ILE* 1.3 57.4 + - - +
305L ARG* 4.0 2.7 - - - -
306L GLY* 3.2 5.4 + - - -
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Residues in contact with ILE 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119L LEU* 3.4 34.1 - - + -
123L ILE* 5.2 2.0 - - + -
134L LEU* 4.9 0.2 - - + -
259L ALA* 3.9 18.2 - - + -
263L LEU* 4.4 6.5 - - + +
264L GLY* 4.5 8.3 - - - -
269L VAL* 4.1 21.3 - - + -
271L ALA* 3.4 33.2 - - + -
295L LEU* 4.7 1.8 - - + -
299L ALA 3.1 17.4 + - - +
300L ALA* 3.6 6.3 - - - +
301L TYR 3.0 0.6 - - - -
302L LEU* 1.3 77.7 - - - +
304L ILE* 1.3 60.1 + - - +
305L ARG 3.1 1.3 - - - -
306L GLY* 3.6 1.9 - - - +
307L MET* 2.8 42.4 + - + +
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Residues in contact with ILE 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L GLU* 3.8 28.5 - - - +
79L THR* 4.4 14.6 - - + +
115L THR* 3.5 25.1 - - - +
118L VAL* 3.9 20.6 - - + -
119L LEU* 3.7 27.8 - - + +
122L LYS* 4.1 7.7 + - + +
300L ALA 3.0 19.9 + - - +
301L TYR* 3.5 17.7 - - + +
303L ILE* 1.3 77.7 - - - +
305L ARG* 1.3 61.8 + - - +
307L MET* 3.6 8.7 + - - +
308L LYS* 3.3 21.2 + - - +
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Residues in contact with ARG 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264I GLY 4.0 7.9 + - - -
266I HIS* 3.4 42.3 + - + +
268I ASP* 2.7 43.7 + - - +
269I VAL* 4.2 3.6 - - - +
302I LEU* 2.7 47.7 + - - +
305I ARG* 3.9 26.6 - - - +
306I GLY* 3.4 21.2 - - - +
301L TYR* 2.8 35.0 + - + +
302L LEU* 4.3 2.5 - - - -
304L ILE* 1.3 77.1 - - - +
306L GLY* 1.3 64.0 + - - +
308L LYS* 3.1 25.1 + - - +
309L THR 4.4 0.2 + - - -
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Residues in contact with GLY 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266I HIS* 5.3 0.2 - - - -
305I ARG* 3.4 13.9 - - - +
263L LEU 3.9 2.7 - - - -
264L GLY 3.8 14.1 - - - -
266L HIS* 4.1 8.7 - - - -
302L LEU 3.2 6.2 + - - -
303L ILE 3.1 5.7 + - - -
305L ARG* 1.3 80.2 - - - +
307L MET* 1.3 59.8 + - - +
308L LYS 3.2 0.6 + - - -
309L THR* 3.5 13.1 + - - -
313L ARG* 2.8 24.8 + - - -
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Residues in contact with MET 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L ALA* 3.4 23.7 - - + +
119L LEU* 3.7 26.5 - - - -
122L LYS* 3.9 23.1 - - + -
123L ILE* 3.9 17.7 - - + -
126L LEU* 3.5 31.9 - - + -
263L LEU* 3.5 32.8 - - + +
303L ILE* 2.8 20.5 + - + +
304L ILE* 3.9 6.3 - - - +
305L ARG 3.2 0.2 - - - -
306L GLY* 1.3 73.3 - - - +
308L LYS* 1.3 60.9 + - - +
309L THR 3.0 7.3 + - - -
310L LEU* 3.2 19.2 + - + +
313L ARG* 4.2 3.6 - - - +
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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