Contacts of the helix formed by residues 301 - 307 (chain M) in PDB entry 2I2X
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 301 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289M LYS* 2.8 40.4 - - - +
300M GLY* 1.3 71.5 - - - -
302M LEU* 1.3 65.7 + - - +
303M VAL 3.2 2.9 - - - -
304M MET* 3.0 29.6 + - + +
356M MET* 3.5 24.7 - - + +
359M SER* 3.1 27.0 + - - +
360M ASP* 2.8 9.3 + - - -
335O TYR* 2.9 31.4 + - - +
339O LEU* 3.8 11.9 + - - +
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Residues in contact with LEU 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274M ILE* 6.0 0.2 - - + -
299M MET* 3.5 14.3 + - + +
301M ASN* 1.3 74.6 - - - +
303M VAL* 1.3 63.0 + - + +
305M GLN* 3.0 60.0 + - - +
356M MET 3.2 16.9 + - - +
357M MET* 3.5 17.9 - - - +
360M ASP* 3.0 19.5 + - + +
361M ARG 4.2 9.4 - - - +
367M ALA* 3.5 23.3 - - + +
370M LEU* 3.6 23.3 - - + +
371M ALA* 3.6 17.5 - - + -
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Residues in contact with VAL 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M TYR* 3.8 19.5 - - + +
286M MET* 3.5 43.4 - - + +
287M GLU 3.3 22.9 - - - +
288M GLY* 3.7 4.3 - - - -
299M MET* 3.4 37.8 + - + +
300M GLY 3.9 2.7 - - - +
302M LEU* 1.3 82.8 - - + +
304M MET* 1.3 60.8 + - - +
305M GLN* 3.0 5.7 + - - +
306M CYS 4.2 1.4 + - - -
307M CYS* 3.7 2.8 + - - +
310M TRP* 3.6 20.0 - - + -
370M LEU* 5.7 2.5 - - + -
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Residues in contact with MET 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M PHE* 3.3 14.4 - - - +
289M LYS* 3.5 17.9 - - + +
301M ASN* 3.0 44.2 + - - +
303M VAL* 1.3 77.4 - - - +
305M GLN* 1.3 65.1 + - - +
306M CYS 2.9 2.4 + - - -
307M CYS* 3.0 19.5 + - - -
310M TRP* 3.3 46.4 - - + -
336M ASP* 4.6 6.1 - - - +
339M LEU* 6.5 0.9 - - + -
340M MET* 4.2 21.3 - - - +
356M MET* 3.6 24.2 - - + +
339O LEU* 5.2 4.5 - - + -
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Residues in contact with GLN 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.4 14.4 + - - -
274M ILE* 3.7 16.8 - - + +
286M MET* 6.1 0.2 - - - +
301M ASN 4.1 0.2 + - - -
302M LEU* 3.0 28.8 + - - +
303M VAL* 3.0 4.5 - - - +
304M MET* 1.3 79.0 - - - +
306M CYS* 1.3 79.0 + - + +
353M ARG* 3.3 33.6 - - + +
356M MET* 3.6 13.2 - - + +
357M MET* 3.4 16.7 - - + +
370M LEU 2.7 27.3 + - - -
371M ALA* 3.7 1.2 - - - -
372M TYR* 2.9 32.4 + - + +
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Residues in contact with CYS 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M MET* 3.9 27.8 - - + -
18M THR 3.7 13.7 - - - +
19M PHE* 3.6 8.1 - - - +
274M ILE* 3.8 23.6 - - + +
277M LYS* 2.8 34.7 + - - +
284M MET* 5.7 1.0 - - - +
286M MET* 5.2 1.3 - - - +
303M VAL 4.2 1.8 + - - -
304M MET 3.1 0.2 - - - -
305M GLN* 1.3 98.5 - - - +
307M CYS* 1.3 63.6 + - - +
308M ASP* 3.6 0.5 - - - +
353M ARG* 4.6 1.3 - - - -
372M TYR* 4.0 11.7 - - - -
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Residues in contact with CYS 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.1 6.2 - - - +
20M GLY 2.7 28.4 + - - -
39M THR* 3.8 4.9 - - - +
284M MET 4.1 0.9 - - - -
286M MET* 3.6 33.0 - - + -
303M VAL 3.7 7.5 + - - +
304M MET* 3.0 22.1 + - - -
306M CYS* 1.3 78.9 - - - +
308M ASP* 1.3 53.3 + - - +
309M CYS 3.8 17.5 - - - +
310M TRP* 4.4 7.9 - - + -
340M MET* 3.7 28.0 - - - -
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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