Contacts of the helix formed by residues 58 - 72 (chain 2) in PDB entry 3EXG
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 58 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1771 GLU* 3.2 36.0 + - - +
1801 ASN* 5.3 0.3 + - - -
1811 MET* 4.3 11.6 - - - +
562 PRO* 3.0 23.6 + - - +
572 ILE* 1.3 74.0 - - - +
592 GLU* 1.3 65.5 + - - +
602 MET 3.4 2.5 - - - -
612 GLY 3.0 0.9 + - - -
622 PHE* 2.8 24.1 + - - -
171Y ASN* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282 GLU* 2.8 28.0 - - - +
572 ILE* 3.7 9.1 - - - +
582 SER* 1.3 71.6 + - - +
602 MET* 1.3 66.1 + - - +
622 PHE* 3.6 20.9 - - + -
632 ALA* 2.9 26.0 + - - +
802 PHE* 4.1 11.4 - - + -
812 MET 5.8 0.7 + - - +
852 PHE* 3.6 42.3 - - + +
882 GLN* 3.0 24.7 + - + +
892 ALA* 4.0 13.0 - - + -
172Y GLN* 3.2 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431 PRO* 4.5 0.3 - - - +
1721 GLN* 5.3 0.7 - - - +
1741 GLN* 3.3 36.3 - - + +
1771 GLU* 3.3 13.2 + - - +
582 SER 3.4 0.6 - - - -
592 GLU* 1.3 78.6 - - - +
612 GLY* 1.3 63.9 + - - +
642 GLY* 3.3 13.7 + - - -
882 GLN* 3.4 40.7 + - + +
892 ALA* 4.2 5.8 - - - +
912 ASP* 3.9 20.6 - - + +
922 GLN* 3.8 20.3 + - - +
60Z MET* 5.7 4.3 - - + -
88Z GLN* 3.5 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 61 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431 PRO* 3.6 13.9 - - - +
1741 GLN* 4.9 0.7 - - - -
1771 GLU* 2.7 26.8 + - - -
1781 ALA 5.1 0.2 - - - -
1811 MET* 3.6 16.6 - - - -
582 SER 3.0 4.5 + - - -
592 GLU 3.0 0.4 + - - -
602 MET* 1.3 77.9 - - - +
622 PHE* 1.3 55.8 + - - +
642 GLY* 3.3 1.4 + - - -
652 ILE* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1811 MET* 3.6 14.1 - - - +
262 LEU* 4.0 10.5 - - + +
272 GLY* 4.4 5.6 - - - -
282 GLU* 3.6 23.6 - - - -
552 THR* 3.4 41.3 - - + -
562 PRO 4.0 2.5 - - - -
582 SER* 2.8 28.1 + - - -
592 GLU* 3.6 28.7 - - + -
612 GLY* 1.3 69.4 - - - -
632 ALA* 1.3 67.6 + - - +
652 ILE* 3.7 7.9 - - + +
662 ALA* 3.1 20.3 + - - +
782 CYS* 3.6 25.4 - - - -
792 GLU 3.9 21.5 - - - -
802 PHE* 4.2 10.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592 GLU 2.9 17.8 + - - +
602 MET 4.1 1.8 - - - +
622 PHE* 1.3 77.7 - - - +
642 GLY* 1.3 59.7 + - - +
662 ALA* 3.0 8.0 + - - +
672 VAL* 2.9 31.2 + - - +
782 CYS* 4.0 12.6 - - - -
802 PHE* 4.2 13.5 - - + -
892 ALA* 3.5 24.2 - - + +
922 GLN* 4.2 9.2 - - + -
932 VAL* 5.5 0.4 - - + -
1142 PHE* 4.8 6.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431 PRO* 3.4 17.2 - - - +
1441 LEU* 3.4 9.2 - - - +
602 MET 3.3 4.4 + - - -
612 GLY 3.3 8.5 + - - -
632 ALA* 1.3 77.9 - - - +
652 ILE* 1.3 55.2 + - - +
672 VAL* 3.3 3.1 + - - -
682 GLY 3.0 23.2 + - - -
922 GLN* 3.6 29.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431 PRO* 3.4 18.4 - - + +
1461 ALA* 4.0 20.6 - - + -
1471 GLY* 3.5 12.2 - - - +
1501 LEU* 4.2 20.9 - - + -
1781 ALA* 5.3 1.8 - - + -
1811 MET* 3.7 30.5 - - + -
1851 TRP* 4.0 24.5 - - + -
1871 LEU* 5.0 2.5 - - + -
262 LEU* 4.6 7.6 - - + -
612 GLY 3.0 14.3 + - - +
622 PHE* 3.8 7.6 - - - +
632 ALA 3.2 0.2 - - - -
642 GLY* 1.3 73.4 - - - +
662 ALA* 1.3 68.1 + - - +
682 GLY 3.1 1.7 + - - -
692 ALA* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 PHE* 5.2 1.1 - - - -
262 LEU* 4.1 9.6 - - + +
622 PHE 3.1 13.8 + - - +
632 ALA 3.0 9.9 + - - +
652 ILE* 1.3 77.9 - - - +
672 VAL* 1.3 64.1 + - - +
692 ALA* 3.1 10.5 + - - -
702 ALA 3.2 8.8 + - - -
762 PRO* 3.2 25.2 - - + +
782 CYS* 3.7 20.9 - - + -
1122 ILE* 3.5 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441 LEU* 3.5 22.0 - - + -
632 ALA 2.9 15.8 + - - +
642 GLY* 3.7 4.3 - - - +
652 ILE 3.2 0.2 - - - -
662 ALA* 1.3 74.4 - - - +
682 GLY* 1.3 63.3 + - - +
702 ALA* 3.1 4.4 + - - +
712 MET* 3.0 26.3 + - - +
922 GLN* 4.1 15.3 - - + +
962 SER* 3.7 26.2 - - - +
972 ALA* 4.2 4.3 - - + -
1102 VAL* 4.1 13.5 - - + -
1122 ILE* 3.7 18.6 - - + -
1142 PHE* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441 LEU* 3.4 32.4 - - - +
1471 GLY* 3.8 7.9 - - - -
1481 ILE* 3.6 9.1 - - - +
642 GLY 3.0 13.0 + - - -
652 ILE 3.1 4.2 + - - -
672 VAL* 1.3 74.9 - - - +
692 ALA* 1.3 62.2 + - - +
712 MET* 3.1 8.8 + - - +
722 ALA 2.9 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471 GLY 3.8 15.7 - - - +
1501 LEU* 4.3 7.9 - - + -
1511 ALA* 4.4 1.9 - - + +
242 PHE* 4.1 30.1 - - + -
652 ILE 3.0 11.1 + - - +
662 ALA 3.7 7.2 - - - +
682 GLY* 1.3 76.5 - - - +
702 ALA* 1.3 59.7 + - - +
722 ALA* 3.3 7.5 + - - +
732 GLY 3.1 5.4 + - - -
742 LEU* 2.8 35.1 + - + +
762 PRO* 4.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662 ALA 3.2 7.3 + - - +
672 VAL 3.1 8.6 + - - +
692 ALA* 1.3 73.0 - - - +
712 MET* 1.3 58.5 + - - +
722 ALA 3.0 1.6 - - - -
732 GLY* 2.6 25.5 + - - -
742 LEU 3.3 10.3 - - - -
762 PRO* 3.8 9.6 - - + +
1092 PRO 4.3 1.0 - - - +
1102 VAL* 4.0 6.5 - - + -
1112 PRO* 3.7 49.0 - - + +
1122 ILE* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861 ILE* 5.7 0.2 - - - -
1271 TYR* 3.9 13.0 - - + +
1321 TYR* 3.3 49.0 + - + +
1351 ASN* 5.0 5.8 - - - +
1441 LEU* 4.2 18.6 - - + -
1481 ILE* 5.0 1.3 - - + -
672 VAL* 3.0 29.5 + - + +
682 GLY* 3.4 9.6 - - - +
702 ALA* 1.3 76.5 - - - +
722 ALA* 1.3 58.2 + - - +
732 GLY 3.3 0.8 + - - -
962 SER* 4.2 8.7 - - - +
1002 THR* 4.2 8.1 - - + +
1082 GLN* 3.3 46.8 + - + +
1092 PRO 4.1 0.9 + - - -
1102 VAL* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841 HIS* 5.0 8.2 - - + +
1321 TYR* 4.0 13.2 - - - +
1481 ILE* 3.9 19.5 - - + +
1511 ALA* 3.7 24.7 - - + +
1551 ASN* 5.1 5.4 + - - -
682 GLY 2.9 13.5 + - - +
692 ALA 3.4 7.0 - - - +
702 ALA 3.0 0.6 - - - -
712 MET* 1.3 77.9 - - - +
732 GLY* 1.3 56.0 + - - +
742 LEU* 3.6 3.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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