Contacts of the helix formed by residues 91 - 98 (chain 3) 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 ALA 91 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 THR* 3.7 26.2 - - + -
883 ALA 4.1 6.7 - - - +
893 TYR 3.6 3.2 + - - -
903 ARG* 1.3 74.8 - - - +
923 HIS* 1.3 71.4 + - - +
933 GLY 3.3 2.7 - - - -
943 PHE* 3.9 4.9 - - - +
953 THR* 2.9 25.7 + - - +
1233 SER 5.4 2.8 + - - +
1243 MET 5.7 0.7 - - - +
1263 MET* 4.8 5.8 - - + +
1313 PHE* 4.0 13.9 - - + -
1343 GLY* 4.3 8.7 - - - +
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Residues in contact with HIS 92 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453 MET* 4.5 6.3 - - - +
463 GLU* 3.0 37.7 + - - +
623 CYS* 4.5 4.3 - - - -
633 HIS 3.3 19.3 + - - -
643 LEU* 3.9 8.0 - - + +
653 CYS* 4.7 0.4 - - - -
893 TYR 5.5 0.8 + - - -
903 ARG 3.7 2.4 + - - -
913 ALA* 1.3 82.4 - - - +
933 GLY* 1.3 66.4 + - - +
953 THR* 3.4 1.1 + - - -
963 PHE* 3.2 17.0 + - - +
1053 ILE* 3.7 19.0 - - + +
1093 LEU* 3.7 30.3 - - + +
1233 SER* 2.7 31.0 + - - -
1263 MET* 3.5 24.9 - - + -
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Residues in contact with GLY 93 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423 VAL* 3.8 20.9 - - - -
653 CYS* 3.6 12.3 - - - -
723 CYS* 3.7 25.1 - - - -
903 ARG 5.2 0.4 + - - -
913 ALA 3.3 0.4 - - - -
923 HIS* 1.3 77.5 - - - +
943 PHE* 1.3 62.5 + - - +
963 PHE* 2.9 6.9 + - - +
973 THR* 2.9 23.4 + - - +
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Residues in contact with PHE 94 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713 CYS 4.5 0.4 - - - -
723 CYS* 3.6 36.1 - - + -
753 LEU* 3.9 19.5 - - + -
763 GLU* 5.8 0.9 - - - -
853 LEU* 3.4 29.8 - - + -
873 THR* 4.4 15.0 - - + -
903 ARG 4.5 13.2 - - - -
913 ALA* 3.5 4.0 + - - +
923 HIS 3.3 0.4 - - - -
933 GLY* 1.3 73.6 - - - +
953 THR* 1.3 66.9 + - - +
963 PHE 3.0 0.9 + - - -
973 THR* 3.2 10.8 + - - -
983 ARG* 3.0 27.6 + - + +
1313 PHE* 3.8 21.1 - - + -
1643 LEU* 3.4 25.6 - - + -
1943 GLU* 3.6 20.6 - - - -
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Residues in contact with THR 95 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913 ALA* 2.9 19.2 + - - +
923 HIS 3.8 0.7 - - - -
943 PHE* 1.3 76.2 - - - +
963 PHE* 1.3 61.3 + - - +
983 ARG* 3.7 5.9 + - - +
993 GLY 3.7 0.7 + - - -
1003 LEU* 3.1 55.6 + - + +
1053 ILE* 3.4 19.7 - - + -
1263 MET* 3.5 23.9 - - + +
1283 ALA* 5.3 1.6 - - + +
1313 PHE* 3.3 29.7 - - + -
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Residues in contact with PHE 96 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383 MET* 4.3 23.6 - - + -
413 THR* 3.3 31.4 - - + -
423 VAL* 3.6 22.9 - - + -
453 MET* 4.3 7.9 - - + -
923 HIS 3.2 11.0 + - - +
933 GLY 2.9 8.7 + - - +
953 THR* 1.3 75.4 - - - +
973 THR* 1.3 67.4 + - + +
983 ARG 3.0 5.2 - - - -
993 GLY* 3.1 13.5 + - - -
1003 LEU 3.3 20.5 - - - +
1013 SER* 5.0 1.6 - - - -
1023 VAL* 3.6 27.6 - - + -
1053 ILE* 3.9 7.0 - - + -
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Residues in contact with THR 97 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383 MET* 5.2 8.3 - - + +
423 VAL* 4.7 3.4 - - + -
723 CYS* 3.4 34.5 + - + +
733 VAL* 3.8 15.0 - - + +
763 GLU* 3.5 41.4 + - - +
933 GLY 2.9 17.1 + - - +
943 PHE* 3.2 22.5 + - - -
963 PHE* 1.3 85.6 - - + +
983 ARG* 1.3 56.3 + - - +
993 GLY 3.3 1.9 + - - -
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Residues in contact with ARG 98 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763 GLU* 3.0 34.2 + - - +
793 ILE* 3.3 15.0 - - - +
803 ASN 3.0 26.7 + - - -
813 PRO* 3.7 13.8 + - - +
833 ASP 2.7 26.1 + - - -
843 HIS* 4.2 2.6 - - - +
853 LEU* 4.2 14.8 - - + +
943 PHE* 3.0 18.0 + - + +
953 THR* 3.9 3.6 - - - +
963 PHE 3.0 1.2 - - - -
973 THR* 1.3 80.6 - - - +
993 GLY* 1.3 56.4 + - - +
1003 LEU 3.7 2.5 + - - -
1283 ALA* 4.2 12.0 - - + +
1293 LYS* 4.2 16.9 + - - +
1303 ASN* 3.5 16.4 + - - +
1313 PHE* 4.1 38.1 - - + -
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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