Contacts of the helix formed by residues 1099 - 1113 (chain A) 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 THR1099 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A GLN* 3.0 31.4 + - - +
1095A TRP* 3.3 18.2 + - + -
1096A TYR 4.1 0.2 - - - -
1098A GLN* 1.3 86.9 - - + +
1100A PRO* 1.3 61.2 - - - +
1101A ASN 3.5 2.2 + - - -
1102A ARG* 4.1 14.3 - - - +
1103A ALA* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A TYR* 3.3 20.3 - - + +
1097A ASN* 3.8 9.2 - - - +
1098A GLN 3.3 10.1 - - - +
1099A THR* 1.3 88.1 - - - +
1101A ASN* 1.3 68.7 + - - +
1103A ALA* 3.5 1.7 + - - +
1104A LYS* 2.9 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A THR 3.5 0.6 - - - -
1100A PRO* 1.3 83.8 - - - +
1102A ARG* 1.3 61.3 + - - +
1104A LYS* 3.1 17.3 + - - +
1105A ARG* 2.9 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A LEU* 4.3 9.3 - - - +
1010A ASP* 3.7 40.0 + - - +
1011A GLU* 3.7 24.6 + - - +
1058A ASN* 2.5 34.3 + - - -
1061A PHE* 4.5 1.2 - - - +
1062A GLN* 3.2 57.9 + - - +
1095A TRP* 5.2 0.2 - - - +
1099A THR* 3.7 15.7 + - - +
1100A PRO 3.5 0.4 - - - -
1101A ASN* 1.3 78.8 - - - +
1103A ALA* 1.3 57.9 + - - +
1105A ARG* 3.3 19.8 + - - +
1106A VAL* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A TRP* 3.7 26.7 - - + -
1096A TYR* 3.7 35.2 - - + -
1099A THR* 3.0 19.9 + - - +
1100A PRO 3.7 4.3 - - - +
1102A ARG* 1.3 76.4 - - - +
1104A LYS* 1.3 57.7 + - - +
1106A VAL* 3.9 0.5 - - - +
1107A ILE* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A TYR* 3.9 30.7 - - + +
1100A PRO* 2.9 32.2 + - - +
1101A ASN* 3.1 17.2 + - - +
1103A ALA* 1.3 76.6 - - - +
1105A ARG* 1.3 56.5 + - + +
1107A ILE* 4.0 4.3 - - - +
1108A THR* 2.5 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A ILE* 4.1 17.1 + - - -
1010A ASP* 2.7 31.2 + - - +
1101A ASN* 2.9 32.1 + - - +
1102A ARG* 3.7 22.1 - - - +
1104A LYS* 1.3 77.2 - - + +
1106A VAL* 1.3 53.0 + - - +
1108A THR* 3.9 2.8 - - - -
1109A THR* 2.5 38.9 + - - -
1117A ALA* 3.9 30.2 - - + +
1118A TYR* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A MET* 5.9 1.1 - - - -
1010A ASP* 4.2 6.1 - - - +
1055A ALA* 4.1 16.6 - - + +
1058A ASN* 4.1 28.9 - - + +
1059A MET* 4.2 3.4 - - + -
1062A GLN* 5.6 0.4 - - - +
1095A TRP* 3.9 24.7 - - + -
1102A ARG* 2.9 26.2 + - + +
1103A ALA 4.0 2.5 - - - +
1105A ARG* 1.3 75.6 - - - +
1107A ILE* 1.3 57.5 + - - +
1109A THR* 3.3 8.3 + - - -
1110A PHE* 2.9 51.6 + - + -
1118A TYR* 4.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087A ALA* 3.5 34.6 - - + +
1090A LEU* 3.8 39.5 - - + +
1091A ALA* 4.4 0.4 - - + +
1095A TRP* 4.2 9.6 - - + -
1096A TYR* 3.7 34.8 - - + -
1103A ALA 2.9 17.9 + - - +
1104A LYS* 4.0 3.1 - - - +
1106A VAL* 1.3 73.0 - - - +
1108A THR* 1.3 63.2 + - - +
1110A PHE* 3.0 12.6 + - - +
1111A ARG* 2.9 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A LYS* 2.5 26.9 + - - +
1105A ARG* 3.9 5.1 - - - -
1107A ILE* 1.3 78.2 - - - +
1109A THR* 1.3 59.0 + - - +
1111A ARG* 2.9 8.5 + - + +
1112A THR* 2.9 43.9 + - + +
1117A ALA* 4.6 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A MET* 5.4 2.2 - - - -
1051A VAL* 3.6 28.3 - - + +
1052A ARG* 3.9 2.3 - - - +
1055A ALA* 4.3 16.4 - - + -
1105A ARG 2.5 24.5 + - - -
1106A VAL* 3.3 8.9 - - - -
1108A THR* 1.3 76.3 - - - +
1110A PHE* 1.3 57.3 + - - +
1112A THR* 4.3 0.9 - - - -
1113A GLY* 2.8 28.1 + - - -
1114A THR 3.8 13.9 + - - +
1115A TRP* 4.9 5.4 - - + -
1117A ALA* 4.3 4.8 - - - +
1118A TYR* 3.3 25.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048A LEU* 3.8 14.6 - - + -
1052A ARG* 2.4 69.7 + - + +
1055A ALA* 3.5 15.3 - - + -
1056A LEU* 3.6 13.7 - - + -
1059A MET* 4.1 15.0 - - - -
1078A LEU* 3.6 38.6 - - + -
1083A TRP* 3.3 14.7 - - + +
1086A ALA* 6.3 1.1 - - + -
1087A ALA* 6.4 0.4 - - + -
1090A LEU* 4.7 12.3 - - + -
1106A VAL* 2.9 38.0 + - + -
1107A ILE* 3.0 12.1 + - + +
1109A THR* 1.3 76.3 - - - +
1111A ARG* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A ARG* 3.0 16.3 + - - -
1083A TRP* 3.6 25.8 + - + +
1084A ASP* 4.9 9.9 - - - +
1087A ALA* 5.7 3.1 - - + -
1107A ILE* 2.9 13.5 + - + +
1108A THR* 2.9 15.0 + - + +
1110A PHE* 1.3 77.9 - - - +
1112A THR* 1.3 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A ARG* 3.2 7.4 + - - -
1108A THR* 2.9 31.4 + - + +
1109A THR* 4.3 0.3 - - - -
1111A ARG* 1.3 77.4 - - + +
1113A GLY* 1.3 65.0 + - - +
1114A THR* 2.9 38.4 + - - +
1116A ASP* 4.8 8.5 - - + +
1117A ALA 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A ASP* 4.5 1.6 - - - +
1051A VAL* 3.4 27.0 - - - +
1052A ARG* 3.3 29.0 - - - +
1109A THR 2.8 18.4 + - - -
1112A THR* 1.3 77.3 + - - +
1114A THR* 1.3 62.8 + - - +
----------------------------------------------------------
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