Contacts of the helix formed by residues 494 - 503 (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 494 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376M TYR* 3.7 3.4 - - - -
493M GLN* 1.3 75.9 - - - +
495M GLU* 1.3 59.2 + - - +
496M GLU* 2.9 26.1 - - - +
497M THR* 2.5 27.9 + - - -
498M ARG* 3.2 8.8 + - - +
1149N GLU* 2.8 17.6 + - - -
99R LEU* 3.3 15.8 - - - +
64S THR* 3.9 10.2 + - - -
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Residues in contact with GLU 495 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376M TYR* 3.4 20.7 + - - +
378M GLU* 5.8 0.3 - - - +
494M SER* 1.3 72.6 + - - +
496M GLU* 1.3 57.4 + - - +
498M ARG* 3.3 31.7 + - - +
499M ALA* 3.6 10.6 + - - +
95R GLY* 4.6 2.6 - - - -
98R ALA* 3.5 27.1 - - + +
99R LEU* 3.7 21.7 - - + +
102R SER* 4.0 11.3 - - - +
116R ASP* 4.8 2.4 - - - +
117R PRO* 3.4 25.7 - - + +
118R LEU* 3.9 19.4 - - - +
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Residues in contact with GLU 496 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494M SER* 2.7 22.0 + - - +
495M GLU* 1.3 74.6 - - - +
497M THR* 1.3 68.0 + - - +
498M ARG 3.4 0.2 - - - -
499M ALA* 3.5 4.0 - - - +
500M GLU* 3.4 19.8 + - - +
1433M MET* 5.5 0.5 - - - +
1145N SER* 3.9 23.0 + - - +
92R ARG* 5.4 5.9 + - - +
95R GLY* 3.7 30.3 + - - +
96R THR* 4.0 13.7 + - - +
99R LEU* 3.6 14.5 - - + +
63S PRO* 3.3 27.2 - - - +
64S THR* 3.5 14.2 - - - -
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Residues in contact with THR 497 (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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492M PRO* 3.2 28.7 - - + -
494M SER* 2.5 17.8 + - - -
496M GLU* 1.3 73.5 - - - +
498M ARG* 1.3 69.5 + - - +
500M GLU* 2.8 22.3 + - - +
501M LEU* 3.2 6.0 + - + +
1145N SER* 4.5 5.5 - - - -
1146N PHE* 3.6 31.5 + - + +
1149N GLU* 2.7 39.6 + - - +
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Residues in contact with ARG 498 (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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376M TYR* 3.2 41.2 + - + +
434M ARG* 4.3 3.8 - - - +
439M ASN 4.8 1.8 + - - -
440M ASP* 3.0 36.6 + - - +
441M PRO* 3.2 47.6 + - + +
492M PRO* 4.1 20.2 - - + +
494M SER 3.2 15.0 - - - +
495M GLU* 3.3 25.5 + - - +
497M THR* 1.3 73.5 - - - +
499M ALA* 1.3 53.8 + - - +
501M LEU* 2.5 31.6 + - - +
502M SER* 2.8 15.3 + - - +
116R ASP* 5.3 6.1 + - - -
118R LEU* 5.8 6.1 - - + +
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Residues in contact with ALA 499 (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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495M GLU 3.6 6.7 + - - +
496M GLU 3.5 11.0 - - - +
498M ARG* 1.3 78.8 - - - +
500M GLU* 1.3 55.7 + - - +
502M SER* 3.3 10.1 + - - -
503M GLN* 2.7 44.9 + - + +
91R ALA 4.0 8.3 - - - +
94R LEU* 5.2 0.2 - - + -
95R GLY* 3.6 29.6 - - - +
118R LEU* 4.8 13.8 - - + +
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Residues in contact with GLU 500 (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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496M GLU 3.4 7.2 + - - +
497M THR* 2.8 18.3 + - - +
499M ALA* 1.3 75.1 - - - +
501M LEU* 1.3 58.7 + - - +
504M LEU* 3.1 33.7 - - + +
505M CYS* 3.6 7.5 - - - -
1438M THR* 3.1 26.5 - - + +
1143N ALA* 2.4 46.0 - - - +
1144N ALA 3.4 1.6 - - - -
1145N SER* 2.5 39.8 + - - -
1146N PHE* 3.0 13.8 + - + +
91R ALA* 5.2 5.4 + - + +
92R ARG* 6.2 0.7 - - - -
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Residues in contact with LEU 501 (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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441M PRO* 4.5 9.6 - - + +
442M VAL 4.6 0.7 - - - -
443M LEU* 4.0 36.8 - - + +
457M ALA* 3.9 14.1 - - + -
490M HIS 5.5 0.2 - - - +
492M PRO* 3.7 39.7 - - + -
497M THR* 3.2 9.6 + - + +
498M ARG* 2.5 15.1 + - - +
500M GLU* 1.3 70.6 - - - +
502M SER* 1.3 62.3 + - - +
505M CYS* 2.5 47.9 + - + -
506M ALA 3.0 5.9 + - - -
1146N PHE* 4.1 24.2 - - + -
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Residues in contact with SER 502 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M PRO* 4.5 16.3 - - - +
457M ALA* 4.9 2.5 - - - -
498M ARG* 2.8 16.2 + - - +
499M ALA* 3.2 15.6 + - - -
501M LEU* 1.3 73.9 - - - +
503M GLN* 1.3 81.5 + - - +
506M ALA* 3.6 22.7 - - - +
509M LEU* 4.1 4.0 - - - +
118R LEU* 4.2 10.4 - - - +
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Residues in contact with GLN 503 (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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499M ALA* 2.7 33.3 + - + +
502M SER* 1.3 107.9 + - - +
504M LEU* 1.3 71.4 + - + +
509M LEU* 3.7 13.5 - - - +
87R LYS* 5.4 3.8 - - - +
90R ARG* 2.7 34.6 + - - +
91R ALA* 4.1 17.6 - - + +
94R LEU* 4.9 9.6 - - + -
118R LEU* 4.9 12.7 - - + +
122R MET* 5.0 5.7 - - - +
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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