Contacts of the helix formed by residues 89 - 96 (chain 4) 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 89 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594 GLU* 3.7 16.4 - - + +
604 MET* 3.8 10.3 - - - +
634 ALA* 3.4 27.6 - - + -
804 PHE* 4.0 13.9 - - + -
864 SER 2.6 13.5 + - - +
884 GLN* 1.3 74.6 - - - +
904 ILE* 1.3 66.0 + - - +
914 ASP 3.2 2.9 - - - -
924 GLN* 3.1 15.8 + - - +
934 VAL* 3.4 11.5 + - - +
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Residues in contact with ILE 90 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864 SER* 3.0 8.8 + - - +
874 MET* 3.3 18.7 + - + +
884 GLN 3.6 0.4 - - - -
894 ALA* 1.3 79.0 - - - +
914 ASP* 1.3 55.6 + - - +
934 VAL* 3.2 5.8 + - - +
944 ILE* 2.7 43.2 + - + +
1324 PHE* 5.3 0.2 - - + -
1354 TRP* 4.1 21.8 - - + -
1364 TYR* 3.4 40.8 - - + +
876 MET* 3.8 29.4 + - + +
906 ILE* 4.3 8.5 - - + -
1356 TRP* 4.0 19.3 - - + -
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Residues in contact with ASP 91 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373 ILE* 3.6 30.8 - - - +
1403 ALA* 3.9 16.3 - - - +
1743 GLN* 5.1 1.9 + - - -
604 MET* 4.8 11.1 - - + +
894 ALA 3.2 0.4 - - - -
904 ILE* 1.3 79.6 - - - +
924 GLN* 1.3 65.5 + - - +
954 ASN* 2.8 53.4 + - - +
964 SER* 3.3 5.4 + - - -
846 ASN 4.8 2.4 - - - +
876 MET* 4.2 20.9 + - + +
886 GLN* 4.6 17.9 - - + +
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Residues in contact with GLN 92 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1403 ALA* 3.4 19.2 + - - +
1433 PRO* 4.0 3.8 - - - +
1443 LEU* 4.0 4.0 - - - +
1743 GLN* 3.3 25.3 + - - -
604 MET* 3.6 29.9 + - - +
634 ALA* 4.0 14.1 - - + +
644 GLY* 3.6 24.8 - - - +
674 VAL* 4.4 5.0 - - + +
894 ALA 3.1 9.8 + - - +
914 ASP* 1.3 83.5 - - - +
934 VAL* 1.3 57.6 + - - +
964 SER* 2.7 37.6 + - - -
974 ALA* 3.0 27.8 + - - +
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Residues in contact with VAL 93 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634 ALA* 5.3 0.4 - - + -
804 PHE* 4.6 11.7 - - + -
894 ALA 3.4 10.1 + - - +
904 ILE* 3.2 11.3 + - - +
924 GLN* 1.3 77.9 - - + +
944 ILE* 1.3 66.1 + - + +
974 ALA* 3.2 8.9 - - - +
984 ALA* 3.1 26.2 + - - +
1144 PHE* 3.5 46.4 - - + -
1364 TYR* 4.0 28.0 - - + +
1424 LEU* 4.2 14.1 - - + -
1684 VAL* 4.6 1.3 - - + -
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Residues in contact with ILE 94 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904 ILE* 2.7 27.6 + - + +
934 VAL* 1.3 77.6 - - + +
954 ASN* 1.3 60.9 - - - +
984 ALA* 3.3 20.5 + - + +
994 LYS* 3.5 29.3 - - - +
1364 TYR* 4.6 4.0 - - + -
1394 CYS* 3.3 39.0 - - + -
1424 LEU* 3.9 19.3 - - + -
876 MET* 4.0 14.1 - - + -
1306 GLN* 3.8 17.5 - - - +
1356 TRP* 4.1 16.8 - - + -
2666 TRP* 5.2 0.2 - - + -
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Residues in contact with ASN 95 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373 ILE* 4.4 9.6 - - + +
914 ASP* 2.8 40.1 + - - +
944 ILE* 1.3 76.1 - - - +
964 SER* 1.3 64.8 + - - +
984 ALA 4.7 0.4 - - - -
994 LYS* 2.9 37.4 + - - +
1004 THR* 4.5 0.2 + - - -
1034 MET* 4.3 8.8 - - - +
846 ASN* 4.6 1.2 + - - +
876 MET* 2.8 31.8 - - - +
1276 GLN* 2.8 47.1 + - - +
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Residues in contact with SER 96 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353 ASN* 5.5 2.5 + - - +
1403 ALA* 4.0 15.6 - - - +
1443 LEU* 4.0 26.3 - - - +
674 VAL* 4.3 6.3 - - - +
714 MET* 5.2 2.0 - - - +
914 ASP* 3.3 3.6 + - - -
924 GLN* 2.7 34.3 + - - -
954 ASN* 1.3 78.6 - - - +
974 ALA* 1.3 60.8 + - - +
1004 THR* 2.6 33.6 + - - -
1104 VAL* 4.6 0.5 - - - +
1276 GLN* 4.7 3.1 + - - +
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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