Contacts of the helix formed by residues 324 - 330 (chain M) in PDB entry 2JA7
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 SER 324 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262M LEU* 5.2 0.4 - - - -
302M THR 3.3 24.7 - - - -
303M TYR* 3.5 5.8 - - - +
304M MET 3.3 11.0 + - - -
305M ASP* 3.9 0.7 - - - -
306M ASN* 3.2 26.6 + - - +
307M ASP* 4.5 2.4 + - - -
322M VAL* 3.1 8.4 + - - -
323M LYS* 1.3 75.8 - - - +
325M ILE* 1.3 69.3 + - - +
326M ARG* 4.3 1.0 - - - +
327M ALA* 2.9 34.2 + - - +
328M ARG* 3.4 5.4 + - - +
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Residues in contact with ILE 325 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246M VAL* 6.2 1.1 - - + -
262M LEU* 3.8 23.3 - - + +
303M TYR* 3.0 36.7 + - + +
304M MET* 3.9 3.4 - - + +
323M LYS 3.9 0.6 + - - -
324M SER* 1.3 70.6 - - - +
326M ARG* 1.3 66.2 + - - +
328M ARG* 2.7 29.3 + - + +
329M LEU* 3.7 4.0 + - + +
1206N GLU* 3.8 20.0 - - + +
1209N ALA* 3.7 29.8 - - + -
1210N MET* 3.2 42.8 - - + -
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Residues in contact with ARG 326 (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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155 T 5.0 9.5 + - - -
304M MET 2.7 23.9 + - - +
305M ASP* 3.1 36.7 + - + -
307M ASP* 5.4 10.7 + - - +
324M SER* 4.3 1.1 - - - +
325M ILE* 1.3 72.0 - - - +
327M ALA* 1.3 63.2 + - - +
329M LEU* 2.8 24.6 + - - +
330M LYS* 3.2 43.1 + - + +
1404M GLU 4.8 0.6 + - - -
1406M VAL* 3.8 31.1 - - + +
1407M GLU* 3.0 50.7 + - - +
1410M PHE* 5.1 3.7 - - + -
1210N MET* 4.1 7.5 - - - -
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Residues in contact with ALA 327 (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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307M ASP* 4.7 10.8 - - - +
322M VAL 5.4 0.7 - - - +
323M LYS* 4.6 10.8 - - + -
324M SER* 2.9 31.6 + - - +
326M ARG* 1.3 83.4 - - - +
328M ARG* 1.3 59.4 + - - +
329M LEU 3.4 0.5 + - - -
330M LYS* 3.7 21.4 + - - +
334M GLY* 5.6 0.7 - - - -
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Residues in contact with ARG 328 (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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246M VAL* 2.7 31.7 + - - +
260M ASP* 3.3 29.1 + - - -
261M ASP* 5.4 1.4 - - - +
262M LEU* 3.2 34.1 - - - +
323M LYS* 5.0 17.1 + - + +
324M SER 4.0 7.0 - - - +
325M ILE* 2.7 25.6 + - + +
327M ALA* 1.3 73.4 - - - +
329M LEU* 1.3 60.6 + - + -
334M GLY* 3.6 5.5 - - - -
335M ARG* 3.4 39.1 + - - +
1114N LEU* 4.3 15.0 - - - +
1206N GLU* 3.2 29.6 + - - +
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Residues in contact with LEU 329 (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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325M ILE* 4.1 7.0 - - + +
326M ARG 2.8 4.5 + - - +
328M ARG* 1.3 80.6 - - + +
330M LYS* 1.3 72.5 + - - +
331M GLY* 3.2 2.4 + - - -
334M GLY 3.5 11.4 - - - +
335M ARG* 3.5 28.7 - - + -
336M ILE* 4.3 5.6 - - + +
1405M THR* 3.9 18.4 - - + +
1406M VAL* 3.5 19.7 - - + -
1409M LEU* 4.7 4.0 - - + -
1203N LEU* 3.8 15.3 - - + +
1206N GLU* 3.6 22.9 - - + +
1207N LEU* 4.1 17.3 - - + -
1210N MET* 3.8 27.6 - - + -
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Residues in contact with LYS 330 (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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155 T 5.0 8.4 + - - +
165 T 3.5 29.4 + - - +
307M ASP* 5.1 16.2 - - - +
326M ARG* 3.2 42.5 + - + +
327M ALA* 3.8 18.0 - - - +
328M ARG 3.6 0.6 - - - -
329M LEU* 1.3 80.1 - - - +
331M GLY* 1.3 74.9 + - - +
332M LYS 3.3 6.9 - - - +
334M GLY* 3.8 6.9 - - - -
1405M THR* 4.4 6.3 - - - +
1406M VAL* 4.4 3.0 - - - +
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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