Contacts of the helix formed by residues 1082 - 1092 (chain B) in PDB entry 5DSG
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 ARG1082 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B MET* 2.8 17.4 + - + +
1080B GLN* 3.6 45.3 + - + +
1081B LYS* 1.3 74.0 - - - +
1083B TRP* 1.3 59.8 + - - +
1084B ASP 3.4 2.0 - - - -
1085B GLU* 3.3 44.5 + - + +
1086B ALA* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1083 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047B SER 5.2 0.2 - - - -
1048B LEU* 3.7 19.7 - - + -
1049B ASP* 5.1 0.7 - - - -
1052B ARG* 3.5 53.5 - - - +
1078B LEU* 3.6 38.6 - - + -
1081B LYS* 3.3 52.0 + - + +
1082B ARG* 1.3 73.4 - - - +
1084B ASP* 1.3 62.5 + - - +
1086B ALA* 3.5 3.4 + - - +
1087B ALA* 2.9 30.0 + - - +
1110B PHE* 3.9 6.8 - - - +
1111B ARG* 3.7 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1084 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082B ARG 3.4 0.2 - - - -
1083B TRP* 1.3 76.5 - - - +
1085B GLU* 1.3 62.7 + - + +
1087B ALA* 3.1 6.4 + - - +
1088B VAL* 2.9 37.7 + - + +
1111B ARG* 3.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1085 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077B MET* 4.6 5.8 - - + +
1082B ARG* 3.3 51.9 + - + +
1083B TRP 3.4 0.2 - - - -
1084B ASP* 1.3 77.9 - - + +
1086B ALA* 1.3 57.4 + - - +
1088B VAL* 3.4 6.3 + - - +
1089B ASN* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074B SER* 4.1 4.4 + - - +
1077B MET* 3.7 21.5 - - + +
1078B LEU* 3.8 31.0 - - + +
1082B ARG 2.9 19.9 + - - +
1083B TRP 3.7 4.5 - - - +
1085B GLU* 1.3 76.7 - - - +
1087B ALA* 1.3 57.1 + - - +
1089B ASN* 3.8 4.3 - - - +
1090B LEU* 2.9 38.1 + - + +
1110B PHE* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B TRP 2.9 18.8 + - - +
1084B ASP* 3.1 6.9 + - - +
1086B ALA* 1.3 73.9 - - - +
1088B VAL* 1.3 61.7 + - + +
1090B LEU* 3.3 5.6 + - - +
1091B ALA* 2.9 28.5 + - - +
1107B ILE* 3.7 29.3 - - + +
1110B PHE* 6.0 1.5 - - + +
1111B ARG* 4.4 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B ASP* 2.9 24.8 + - + +
1085B GLU* 3.8 6.5 - - - +
1087B ALA* 1.3 76.8 - - + +
1089B ASN* 1.3 62.4 + - - +
1091B ALA* 3.2 16.2 + - + +
1092B LYS* 3.4 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1089 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B ASN* 3.5 23.0 + - - +
1074B SER* 2.4 39.3 + - - +
1077B MET* 5.8 0.9 - - + -
1085B GLU 2.9 18.6 + - - +
1086B ALA* 3.9 4.3 - - - +
1088B VAL* 1.3 77.6 - - - +
1090B LEU* 1.3 60.4 + - - +
1092B LYS* 3.6 35.9 + - - +
1093B SER* 4.0 4.2 + - - -
1207B PG6 2.6 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B MET* 4.1 11.0 - - + -
1071B PHE* 3.8 21.8 - - + -
1074B SER* 3.5 25.6 - - - +
1078B LEU* 5.1 7.2 - - + -
1086B ALA* 2.9 27.2 + - + +
1087B ALA* 3.7 2.2 - - - +
1088B VAL 3.2 0.2 - - - -
1089B ASN* 1.3 75.1 - - - +
1091B ALA* 1.3 60.1 + - - +
1092B LYS 3.2 0.9 - - - -
1093B SER* 2.8 24.0 + - - -
1095B TRP* 4.1 17.3 - - + -
1096B TYR* 3.7 4.5 - - - +
1107B ILE* 3.5 30.4 - - + +
1110B PHE* 4.0 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087B ALA 2.9 17.3 + - - +
1088B VAL* 3.2 10.9 + - + +
1090B LEU* 1.3 79.1 - - - +
1092B LYS* 1.3 57.7 - - + +
1093B SER 3.3 1.7 - - - +
1096B TYR* 3.3 35.9 - - + +
1107B ILE* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088B VAL* 3.4 19.6 - - + +
1089B ASN* 3.6 38.8 + - - +
1090B LEU 3.2 0.8 - - - -
1091B ALA* 1.3 79.5 - - + +
1093B SER* 1.3 62.2 + - - +
----------------------------------------------------------
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