Contacts of the helix formed by residues 68 - 76 (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 GLN 68 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653 CYS* 2.8 24.9 + - + +
673 GLY* 1.3 81.9 - - - +
693 GLU* 1.3 57.5 + - - +
703 ALA* 3.1 3.8 - - - -
713 CYS* 2.8 35.4 + - + +
723 CYS* 3.7 5.4 + - - -
903 ARG* 3.9 15.2 - - - +
1943 GLU* 3.3 30.1 - - - +
1963 ASN* 3.6 10.1 + - - +
2273 GLY 5.4 1.3 - - - -
2573 THR* 3.3 28.3 - - + +
2583 TYR 4.5 0.7 - - - +
2593 ARG* 2.8 46.1 - - + +
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Residues in contact with GLU 69 (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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393 MET* 3.8 34.5 - - + +
423 VAL* 3.7 25.4 - - + +
433 ARG* 2.8 46.7 + - - -
653 CYS 4.1 1.1 - - - +
663 ASP* 3.2 9.8 - - - +
673 GLY 3.0 23.2 + - - -
683 GLN* 1.3 75.0 + - - +
703 ALA* 1.3 62.2 + - - +
713 CYS 3.2 0.2 + - - -
723 CYS* 4.0 8.7 - - - -
733 VAL* 2.3 39.2 + - + +
2873 PRO* 3.3 10.3 - - + +
2883 ILE* 4.7 1.3 - - - -
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Residues in contact with ALA 70 (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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393 MET* 4.4 7.9 - - - -
673 GLY 5.6 0.2 - - - +
683 GLN 3.1 1.7 - - - +
693 GLU* 1.3 80.4 - - - +
713 CYS* 1.3 58.1 + - - +
743 GLY* 2.8 27.4 + - - -
2273 GLY 3.0 29.4 - - - +
2283 MET* 3.5 23.1 - - - +
2303 ILE* 3.8 14.6 - - - +
2333 VAL* 4.0 6.6 - - + +
2873 PRO* 3.9 11.0 - - + +
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Residues in contact with CYS 71 (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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683 GLN* 2.8 21.5 + - - +
703 ALA* 1.3 68.5 - - - +
723 CYS* 1.3 74.1 + - - +
743 GLY 2.9 0.5 + - - -
753 LEU* 2.9 27.7 + - + +
943 PHE* 4.6 0.9 - - + -
1943 GLU* 4.1 21.5 - - - +
2273 GLY* 4.1 16.2 - - - -
2333 VAL* 4.3 7.4 - - - -
2553 LEU* 3.6 38.6 - - + -
2573 THR* 5.2 6.7 - - - -
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Residues in contact with CYS 72 (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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423 VAL* 4.3 9.6 - - - -
653 CYS* 5.2 5.2 - - - -
683 GLN 3.7 2.4 + - - -
693 GLU* 4.0 20.6 - - - -
713 CYS* 1.3 84.1 - - - +
733 VAL* 1.3 62.8 + - - +
753 LEU* 4.0 2.1 - - - +
763 GLU* 3.0 25.6 + - - +
933 GLY* 3.7 31.6 - - - -
943 PHE* 3.6 25.7 - - + +
973 THR* 3.4 26.6 + - + +
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Residues in contact with VAL 73 (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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353 TYR* 4.1 13.8 - - + +
383 MET* 3.3 49.4 - - + +
393 MET* 3.4 24.0 - - + +
423 VAL* 5.9 1.1 - - + -
693 GLU* 2.3 38.1 - - + +
703 ALA 4.0 0.7 - - - +
723 CYS* 1.3 77.9 - - - +
743 GLY* 1.3 60.1 + - - +
763 GLU* 3.7 5.1 + - - +
773 ALA* 3.3 18.7 + - - +
973 THR* 3.8 9.4 - - + +
2303 ILE* 3.8 11.1 - - + +
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Residues in contact with GLY 74 (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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703 ALA 2.8 22.3 + - - -
733 VAL* 1.3 72.4 - - - +
753 LEU* 1.3 66.6 + - - +
763 GLU 3.1 1.1 - - - -
773 ALA* 3.1 19.1 + - - +
783 GLY 3.3 6.1 + - - -
2303 ILE* 3.5 13.9 - - - -
2333 VAL* 3.6 13.5 - - - -
2343 ARG* 3.4 14.8 - - - -
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Residues in contact with LEU 75 (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* 2.9 17.1 + - + +
723 CYS 4.0 1.8 - - - +
743 GLY* 1.3 75.6 - - - +
763 GLU* 1.3 62.3 + - - +
773 ALA 2.9 2.6 + - - -
783 GLY* 3.1 10.2 + - - -
793 ILE* 3.2 17.1 + - - +
853 LEU* 5.0 3.1 - - + -
943 PHE* 3.9 27.8 - - + -
1623 LEU* 3.9 21.3 - - + -
1643 LEU* 4.4 5.8 - - + -
1923 ILE* 4.1 17.7 - - + -
2333 VAL* 3.1 29.8 - - + -
2373 THR* 3.2 22.2 - - - +
2533 MET* 3.8 11.7 - - + -
2553 LEU* 4.2 15.7 - - + -
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Residues in contact with GLU 76 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383 MET* 5.7 6.3 - - - -
723 CYS 3.0 17.7 + - - +
733 VAL* 3.8 8.7 - - + +
743 GLY 3.1 0.2 - - - -
753 LEU* 1.3 80.1 - - - +
773 ALA* 1.3 57.7 + - - +
783 GLY 3.4 0.2 - - - -
793 ILE* 3.4 24.9 - - - +
803 ASN 4.4 2.1 - - - +
813 PRO* 4.8 2.8 - - - +
853 LEU* 5.6 3.1 - - - +
943 PHE* 5.8 1.0 - - - -
973 THR* 3.5 39.1 + - - +
983 ARG* 3.0 43.8 + - - +
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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