Contacts of the helix formed by residues 296 - 307 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ASN* 4.8 5.1 + - - -
294F ALA 3.9 2.4 + - - -
295F LEU* 1.3 75.7 - - - +
297F PRO* 1.3 68.9 - - - +
298F ASN* 3.0 39.7 + - - +
299F ALA* 2.7 27.5 + - + +
300F ALA* 2.9 10.1 + - - +
268H ASP 5.2 1.4 + - - -
269H VAL* 4.2 15.2 - - - +
270H LEU 5.2 2.2 + - - +
296H ASN* 3.9 25.2 - - + +
298H ASN* 4.5 0.9 - - - +
299H ALA* 3.9 23.7 - - + +
302H LEU* 5.6 1.2 - - - +
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Residues in contact with PRO 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F VAL* 3.9 10.0 - - + +
82F VAL 3.2 12.8 - - - +
83F ASN* 4.4 7.0 - - - +
84F THR 5.3 1.8 - - - +
113F ASN* 3.0 30.5 - - + +
115F THR* 3.3 28.9 + - + -
116F THR* 4.5 1.6 - - - +
295F LEU 3.6 5.3 - - - +
296F ASN* 1.3 97.0 - - - +
298F ASN* 1.3 60.9 + - - +
300F ALA* 3.2 8.8 + - + +
301F TYR* 3.0 23.7 + - - +
268H ASP 6.1 0.2 - - - +
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Residues in contact with ASN 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E ASN* 5.5 2.9 - - - +
81F VAL* 3.6 18.2 - - - +
83F ASN* 3.3 27.8 + - - +
296F ASN* 3.0 17.8 + - - +
297F PRO* 1.3 78.5 - - - +
299F ALA* 1.3 61.3 + - - +
301F TYR* 3.5 4.9 + - - +
302F LEU* 3.2 26.9 + - - +
298H ASN* 3.7 36.3 - - + +
302H LEU* 4.6 11.1 - - - +
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Residues in contact with ALA 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F VAL* 3.4 27.7 - - + +
270F LEU 4.6 0.9 - - - +
295F LEU* 4.1 16.6 - - + -
296F ASN* 2.7 14.2 + - + +
298F ASN* 1.3 77.7 - - - +
300F ALA* 1.3 65.1 + - - +
302F LEU* 3.0 18.7 + - - +
303F ILE* 3.1 17.3 + - - +
296H ASN* 3.9 18.7 + - + +
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Residues in contact with ALA 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F THR 3.8 18.2 - - - +
116F THR* 3.9 15.5 - - - +
119F LEU* 3.8 10.3 - - + +
295F LEU* 3.6 25.0 - - + +
296F ASN 2.9 8.5 + - - +
297F PRO* 3.2 11.0 + - + +
299F ALA* 1.3 76.5 - - - +
301F TYR* 1.3 55.6 + - - +
303F ILE* 3.4 3.9 + - - +
304F ILE* 3.0 32.8 + - - +
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Residues in contact with TYR 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ASN* 3.8 20.0 + - + -
78F THR* 4.1 7.9 - - + +
79F THR* 3.5 41.7 - - + -
81F VAL* 4.0 22.9 - - + -
115F THR* 4.5 3.1 + - - +
297F PRO 3.0 14.8 + - - +
298F ASN* 3.8 5.2 - - - +
299F ALA 3.1 0.2 - - - -
300F ALA* 1.3 71.6 - - - +
302F LEU* 1.3 69.8 + - + +
303F ILE 3.0 1.8 - - - -
304F ILE* 3.5 14.9 - - + +
305F ARG* 2.8 50.0 + - + +
266G HIS 5.2 0.2 + - - -
268G ASP* 2.7 42.2 + - - +
302G LEU* 5.0 8.5 - - + -
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Residues in contact with LEU 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F GLY 4.8 0.3 - - - +
268F ASP* 4.0 26.0 - - - +
269F VAL* 4.2 11.4 - - + -
298F ASN 3.2 14.8 + - - +
299F ALA* 3.0 12.7 + - - +
301F TYR* 1.3 87.0 - - + +
303F ILE* 1.3 58.3 + - - +
305F ARG* 4.5 2.7 - - - -
306F GLY* 3.2 7.1 + - - -
301G TYR* 4.9 8.7 - - + -
302G LEU* 5.1 10.3 - - + -
305G ARG* 2.7 59.6 + - - +
83H ASN* 4.3 18.2 - - - +
296H ASN* 5.5 0.9 - - - +
298H ASN* 4.5 9.0 - - - +
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Residues in contact with ILE 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F LEU* 3.4 35.9 - - + -
123F ILE* 5.2 1.3 - - + -
134F LEU* 4.6 1.1 - - + -
259F ALA* 3.8 18.4 - - + -
263F LEU* 4.2 7.0 - - + +
264F GLY* 4.6 9.0 - - - -
269F VAL* 4.0 20.4 - - + -
271F ALA* 3.3 33.9 - - + -
295F LEU* 4.9 1.8 - - + -
299F ALA 3.1 15.1 + - - +
300F ALA* 3.7 6.7 - - - +
301F TYR 3.0 0.4 - - - -
302F LEU* 1.3 75.1 - - - +
304F ILE* 1.3 66.6 + - - +
305F ARG 3.0 1.6 - - - -
306F GLY* 2.9 2.1 + - - -
307F MET* 2.9 34.2 + - + +
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Residues in contact with ILE 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F GLU* 3.9 28.5 - - - +
79F THR* 4.3 14.6 - - + +
115F THR* 3.5 25.1 - - - +
118F VAL* 3.7 22.0 - - + -
119F LEU* 3.8 25.1 - - + +
122F LYS* 4.1 9.5 + - + +
300F ALA 3.0 17.3 + - - +
301F TYR* 3.5 16.6 - - + +
303F ILE* 1.3 76.6 - - - +
305F ARG* 1.3 62.9 + - - +
307F MET* 3.4 9.8 + - - +
308F LYS* 3.4 20.4 + - - +
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Residues in contact with ARG 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F HIS* 6.0 0.2 + - - -
301F TYR* 2.8 34.2 + - + +
302F LEU* 4.3 2.0 - - - +
304F ILE* 1.3 78.2 - - - +
306F GLY* 1.3 64.6 + - - +
308F LYS* 3.1 26.0 + - + +
264G GLY 3.8 6.7 + - - -
266G HIS* 3.5 47.8 + - + +
268G ASP* 2.7 41.2 + - - +
269G VAL* 4.5 3.4 - - - +
302G LEU* 2.9 45.5 + - - +
305G ARG* 3.9 28.0 - - - +
306G GLY* 3.4 20.4 - - - +
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Residues in contact with GLY 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F LEU 4.0 2.0 - - - -
264F GLY 4.0 13.9 - - - -
266F HIS* 4.0 9.4 - - - -
302F LEU 3.2 6.5 + - - -
303F ILE 2.9 7.1 + - - -
305F ARG* 1.3 79.6 - - - +
307F MET* 1.3 59.4 + - - +
308F LYS 3.1 1.4 + - - -
309F THR* 3.3 12.9 + - - -
313F ARG* 2.9 23.3 + - - -
266G HIS* 5.4 0.2 - - - -
305G ARG* 3.6 13.2 - - - +
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Residues in contact with MET 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ALA* 3.1 29.0 - - + +
119F LEU* 3.7 26.7 - - - -
122F LYS* 4.0 20.6 - - + -
123F ILE* 3.9 20.0 - - + -
126F LEU* 3.6 30.7 - - + -
263F LEU* 3.5 38.6 - - + +
303F ILE* 2.9 16.2 + - - +
304F ILE 3.8 6.1 - - - +
305F ARG 3.2 0.6 - - - -
306F GLY* 1.3 72.2 - - - +
308F LYS* 1.3 60.1 + - - +
309F THR 3.0 7.5 + - - -
310F LEU* 3.2 19.2 + - + +
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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
------------------------------------------------------------
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