Contacts of the helix formed by residues 91 - 98 (chain 5) 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 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875 THR* 3.5 27.4 - - + -
885 ALA 4.0 0.7 - - - +
895 TYR 3.0 6.8 + - - -
905 ARG* 1.3 74.1 - - - +
925 HIS* 1.3 70.3 + - - +
935 GLY 3.5 1.3 - - - -
945 PHE* 3.4 5.0 + - - -
955 THR* 2.9 25.9 + - - +
1235 SER 5.5 0.7 - - - +
1245 MET 5.3 1.8 - - - +
1265 MET* 4.6 5.8 - - + +
1315 PHE* 4.0 7.0 - - + -
1345 GLY* 3.9 24.2 - - - +
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Residues in contact with HIS 92 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 MET* 4.9 7.6 - - - -
465 GLU* 3.0 32.6 + - - +
495 ALA* 5.4 0.2 - - + -
625 CYS* 4.3 7.6 - - - -
635 HIS 3.2 29.6 + - - -
645 LEU* 3.9 7.9 - - + -
655 CYS* 5.3 0.2 - - - -
895 TYR 4.9 1.8 + - - -
905 ARG 3.6 2.0 - - - -
915 ALA* 1.3 72.8 - - - +
935 GLY* 1.3 69.7 + - - +
955 THR* 2.9 16.0 + - - -
965 PHE* 3.0 13.5 + - - +
1055 ILE* 4.5 14.7 - - + +
1095 LEU* 4.1 16.2 - - + +
1235 SER* 2.9 31.2 + - - -
1265 MET* 3.3 28.3 - - + -
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Residues in contact with GLY 93 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425 VAL* 3.8 21.0 - - - +
455 MET* 6.1 0.2 - - - -
465 GLU* 5.1 0.2 - - - -
655 CYS* 3.7 27.6 - - - -
725 CYS* 4.0 10.1 - - - -
905 ARG 4.8 0.2 + - - -
915 ALA 3.5 0.4 - - - -
925 HIS* 1.3 78.8 - - - +
945 PHE* 1.3 56.3 + - - +
965 PHE* 3.5 1.9 + - - +
975 THR* 3.0 33.8 + - - +
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Residues in contact with PHE 94 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655 CYS* 6.1 4.0 - - + -
685 GLN* 5.8 0.9 - - - -
715 CYS* 4.8 0.7 - - + -
725 CYS* 3.5 35.9 - - + -
755 LEU* 3.7 15.5 - - + -
855 LEU* 3.6 23.1 - - + -
875 THR* 4.4 11.2 - - + -
905 ARG 4.2 17.3 - - - -
915 ALA* 3.4 6.8 + - - +
925 HIS 3.0 0.8 - - - -
935 GLY* 1.3 76.3 - - - +
955 THR* 1.3 64.6 + - - +
975 THR* 3.2 8.6 + - - -
985 ARG* 3.0 28.8 + - - +
1315 PHE* 4.0 18.8 - - + -
1645 LEU* 3.2 30.1 - - + -
1945 GLU* 3.7 27.1 - - - -
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Residues in contact with THR 95 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915 ALA* 2.9 14.8 + - - +
925 HIS* 2.9 11.0 + - - -
945 PHE* 1.3 71.7 - - - +
965 PHE* 1.3 69.5 + - - +
985 ARG* 3.5 8.4 + - - +
995 GLY 3.5 0.5 + - - -
1005 LEU* 3.0 55.5 + - + +
1055 ILE* 3.6 15.7 - - + -
1265 MET* 3.6 26.5 - - + +
1285 ALA* 5.0 1.6 - - + -
1315 PHE* 3.5 21.8 - - + -
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Residues in contact with PHE 96 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385 MET* 3.9 29.8 - - + -
415 THR* 3.5 36.8 - - + -
425 VAL* 3.8 22.2 - - + -
455 MET* 4.8 4.5 - - + -
925 HIS 3.0 10.5 + - - +
935 GLY* 3.7 7.2 - - - +
955 THR* 1.3 76.3 - - - +
975 THR* 1.3 61.1 + - + +
985 ARG 2.7 12.6 + - - -
995 GLY* 2.7 17.7 + - - -
1005 LEU 3.6 19.5 + - - +
1015 SER* 5.2 0.7 - - - -
1025 VAL* 3.7 26.2 - - + -
1055 ILE* 3.8 13.2 - - + +
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Residues in contact with THR 97 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385 MET* 5.0 11.4 - - - +
425 VAL* 4.4 2.2 - - + -
725 CYS* 3.5 38.6 + - - +
735 VAL* 4.1 14.6 - - + -
765 GLU* 3.3 32.4 + - - +
935 GLY 3.0 16.2 + - - +
945 PHE* 3.2 18.5 + - - -
965 PHE* 1.3 88.6 - - + +
985 ARG* 1.3 57.6 + - - +
995 GLY 3.3 0.4 + - - -
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Residues in contact with ARG 98 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765 GLU* 2.8 40.3 + - - -
795 ILE* 3.4 12.7 - - - +
805 ASN 3.4 21.0 + - - -
815 PRO* 3.6 9.4 + - - +
835 ASP 3.0 16.7 + - - -
855 LEU* 4.0 17.1 - - - +
945 PHE* 3.0 18.0 + - - +
955 THR 3.9 5.2 - - - +
965 PHE 2.7 6.1 + - - -
975 THR* 1.3 76.2 - - - +
995 GLY* 1.3 55.2 + - - +
1005 LEU 3.8 1.3 - - - -
1285 ALA* 4.3 8.6 - - + +
1295 LYS* 3.8 17.0 + - - +
1305 ASN* 2.6 37.9 + - - +
1315 PHE* 3.3 39.0 - - + -
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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
------------------------------------------------------------
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