Contacts of the helix formed by residues 741 - 750 (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 ASN 741 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667M GLY 4.5 0.3 - - - +
668M ASP* 2.7 41.4 + - - +
737M LEU* 3.6 29.6 - - + +
738M LYS* 3.0 16.5 + - + +
740M LEU* 1.3 88.5 + - + +
742M ASN* 1.3 62.5 + - - +
743M VAL* 2.7 41.2 - - - +
744M LYS* 2.8 16.7 + - + +
745M GLN* 3.1 19.8 + - - +
192O TRP* 4.3 3.1 - - + +
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Residues in contact with ASN 742 (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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533M LYS* 5.8 0.2 + - - -
662M PHE* 3.7 14.7 - - + -
663M SER 3.0 31.7 + - - +
664M THR* 3.3 9.3 - - - +
668M ASP* 2.6 37.2 + - - +
740M LEU 3.0 2.9 + - - +
741M ASN* 1.3 67.9 - - - +
743M VAL* 1.3 65.6 + - - +
745M GLN* 2.8 32.0 + - - +
746M MET* 2.9 14.8 + - - +
1069N PHE* 3.9 10.1 - - - -
1083N ALA* 5.4 5.7 - - - +
1084N GLN 5.5 2.6 + - - +
192O TRP* 3.5 18.1 - - - +
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Residues in contact with VAL 743 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664M THR* 4.0 18.6 + - + +
668M ASP* 3.9 23.5 + - + +
669M THR* 5.3 2.5 - - + -
737M LEU* 5.7 1.6 - - + -
741M ASN* 2.7 14.8 - - - +
742M ASN* 1.3 74.0 - - - +
744M LYS* 1.3 63.0 + - - +
746M MET* 3.3 12.5 + - - +
747M VAL* 2.9 27.7 + - + +
757M ASN* 6.2 1.3 - - + -
758M ILE* 4.1 25.8 - - + +
761M MET* 4.6 21.5 - - + -
1017N ILE* 5.3 2.0 - - + -
1018N PRO* 4.4 21.0 - - + +
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Residues in contact with LYS 744 (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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734M GLU* 4.1 21.4 + - + +
735M VAL* 5.3 3.6 + - - +
737M LEU* 3.2 35.2 + - + +
738M LYS 4.1 5.6 - - - +
739M ASP* 3.7 14.9 + - - -
741M ASN* 2.8 25.0 - - + +
743M VAL* 1.3 73.9 - - - +
745M GLN* 1.3 57.7 + - - +
747M VAL* 2.6 34.5 + - + +
748M MET* 2.7 40.9 + - + +
758M ILE* 5.0 8.1 - - + -
19T ARG* 4.0 13.7 - - - +
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Residues in contact with GLN 745 (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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529M CYS* 5.5 2.7 - - - -
532M ARG* 3.7 26.5 + - - +
533M LYS* 3.2 40.2 + - - +
536M LEU* 6.1 0.6 - - - +
662M PHE* 3.7 12.3 - - + -
739M ASP 4.1 14.6 + - - +
740M LEU* 3.2 21.7 - - - +
741M ASN 3.1 9.6 + - - +
742M ASN* 2.8 30.4 + - - +
744M LYS* 1.3 78.6 - - - +
746M MET* 1.3 60.7 + - - +
748M MET* 3.0 14.1 + - + +
749M ALA* 2.9 23.3 + - - +
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Residues in contact with MET 746 (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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529M CYS* 4.3 3.1 - - - -
662M PHE* 3.8 24.2 - - + -
664M THR* 3.5 25.1 - - - +
742M ASN 2.9 6.6 + - - +
743M VAL* 3.5 11.7 - - - +
745M GLN* 1.3 75.7 - - - +
747M VAL* 1.3 66.5 + - - +
748M MET 3.0 0.3 + - - -
749M ALA* 3.0 4.3 + - - +
750M GLY 2.9 19.8 + - - -
751M SER* 3.5 19.6 + - - +
752M LYS* 3.6 12.9 - - - +
1014N PRO* 3.7 10.1 - - + +
1015N HIS* 3.1 39.0 - - + -
1018N PRO* 3.3 37.0 - - + -
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Residues in contact with VAL 747 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734M GLU* 5.8 3.1 - - - +
743M VAL* 2.9 23.9 + - + +
744M LYS* 2.6 23.4 + - + +
746M MET* 1.3 72.2 - - - +
748M MET* 1.3 59.4 + - + +
750M GLY* 3.6 9.4 + - - +
752M LYS 3.6 8.3 + - - +
753M GLY* 3.8 24.1 - - - +
754M SER* 4.1 14.8 - - - +
755M PHE* 4.5 2.5 - - - +
758M ILE* 4.0 21.5 - - + -
1018N PRO* 6.0 0.4 - - + -
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Residues in contact with MET 748 (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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532M ARG* 3.5 38.8 - - - +
618M GLU* 3.9 16.1 - - - +
620M LYS* 5.4 2.6 + - - -
739M ASP* 4.4 27.4 - - + +
744M LYS* 2.7 47.3 + - + +
745M GLN* 3.0 24.9 + - + +
747M VAL* 1.3 73.6 - - + +
749M ALA* 1.3 65.8 + - - +
750M GLY* 3.1 2.6 + - - -
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Residues in contact with ALA 749 (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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528M LEU* 3.8 5.6 - - + +
529M CYS* 3.8 31.4 - - - +
532M ARG* 4.0 21.5 - - + +
618M GLU* 3.6 5.2 - - - +
619M LYS* 3.3 28.8 + - - +
745M GLN 2.9 11.9 + - - +
746M MET* 3.6 8.3 - - - +
748M MET* 1.3 77.9 - - - +
750M GLY* 1.3 60.8 + - - +
751M SER* 3.9 8.1 - - - +
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Residues in contact with GLY 750 (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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528M LEU* 3.8 6.7 - - - +
618M GLU* 5.6 0.2 - - - -
619M LYS* 3.6 34.3 + - - +
746M MET 2.9 7.2 + - - -
747M VAL* 3.9 9.2 - - - -
748M MET 3.1 3.5 - - - -
749M ALA* 1.3 80.6 - - - +
751M SER* 1.3 63.2 + - - +
752M LYS* 3.3 3.7 - - - -
753M GLY 5.8 0.9 - - - -
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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