Contacts of the helix formed by residues 1089 - 1102 (chain A) in PDB entry 1Y8Z
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 GLN1089 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A ALA* 5.9 1.8 - - + -
1087A SER 5.3 1.8 - - - +
1088A VAL* 1.3 81.1 - - - +
1090A GLU* 1.3 68.0 + - - +
1091A ALA* 3.1 9.0 - - + +
1092A THR* 3.0 23.4 + - - +
1093A ILE* 3.5 5.1 + - - +
3005A NCO 3.9 4.9 - - - -
1246B LYS* 5.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1090 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089A GLN* 1.3 73.2 - - - +
1091A ALA* 1.3 49.7 + - - +
1093A ILE* 3.3 9.2 - - - +
1094A ASN* 2.7 64.3 + - - +
3005A NCO 2.9 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1091 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A ALA* 3.9 28.3 - - + +
1089A GLN* 3.1 7.0 + - + +
1090A GLU* 1.3 78.2 - - - +
1092A THR* 1.3 57.8 - - - +
1094A ASN* 3.7 6.5 - - - +
1095A ASN* 3.0 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1092 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A ALA 5.7 0.7 - - - +
1039A ALA* 5.7 0.2 - - + -
1041A ASP* 2.7 43.0 + - + +
1061A LEU* 4.0 15.5 - - + +
1062A ALA* 3.5 14.7 - - - +
1084A PRO* 4.5 7.6 - - + -
1088A VAL* 3.7 26.7 - - + +
1089A GLN* 3.0 16.0 + - - +
1091A ALA* 1.3 76.0 - - - +
1093A ILE* 1.3 65.8 + - - +
1095A ASN 3.5 0.3 + - - -
1096A TYR* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1093 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A PRO* 4.4 5.4 - - + -
1088A VAL* 4.1 4.0 - - + +
1089A GLN 3.5 3.3 + - - +
1090A GLU* 3.3 28.7 - - - +
1092A THR* 1.3 80.1 - - - +
1094A ASN* 1.3 74.8 + - - +
1096A TYR* 4.0 11.9 - - + -
1097A LYS* 3.0 51.3 + - + +
1125A LEU* 3.7 60.3 - - + +
1126A GLY* 3.8 4.9 - - - +
3005A NCO 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1094 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090A GLU* 2.7 46.3 + - - +
1091A ALA* 3.7 7.3 + - - +
1093A ILE* 1.3 87.1 - - - +
1095A ASN* 1.3 62.4 + - - +
1097A LYS* 3.5 11.0 + - - +
1098A LYS* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1095 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A LEU* 2.7 33.4 + - + +
1062A ALA 3.2 17.6 + - - -
1063A LYS* 5.0 0.2 - - - +
1065A TYR* 3.6 25.4 - - + +
1091A ALA* 3.0 17.2 + - - +
1092A THR 4.2 0.2 - - - +
1094A ASN* 1.3 76.7 - - - +
1096A TYR* 1.3 62.4 + - - +
1098A LYS* 3.0 32.7 + - - +
1099A LEU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1096 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A PHE* 4.1 17.3 - + - -
1008A ALA* 3.5 27.8 - - + -
1061A LEU* 3.8 15.4 - - + +
1080A ILE* 3.7 8.3 - - + +
1083A VAL* 3.6 12.7 - - + +
1084A PRO* 3.7 24.2 - - + -
1092A THR 3.0 19.0 + - - +
1093A ILE* 3.6 13.7 - - + +
1095A ASN* 1.3 77.2 - - - +
1097A LYS* 1.3 65.7 + - + +
1099A LEU* 3.0 23.5 + - + +
1100A LEU* 3.2 36.3 + - + +
1126A GLY* 4.1 6.5 - - - -
1130A THR* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1097 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093A ILE* 3.0 47.0 + - + +
1094A ASN* 3.8 9.7 - - - +
1096A TYR* 1.3 80.2 - - + +
1098A LYS* 1.3 62.3 + - - +
1100A LEU* 3.3 10.7 + - - +
1101A ASP* 3.3 28.0 + - - +
1126A GLY* 4.2 4.7 - - - +
1129A GLU* 3.4 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1098 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A TYR* 3.4 36.6 - - + +
1094A ASN* 3.0 14.5 + - - +
1095A ASN* 3.0 35.3 + - - +
1096A TYR 3.1 0.4 - - - -
1097A LYS* 1.3 76.7 - - - +
1099A LEU* 1.3 63.4 + - - +
1101A ASP* 3.3 7.6 + - - +
1102A ASN* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1099 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A PHE* 4.2 26.2 - - + -
1061A LEU* 4.4 8.3 - - + -
1065A TYR* 3.7 12.8 - - + -
1068A ALA* 3.8 21.3 - - + +
1069A LEU* 3.4 48.1 - - + +
1072A VAL* 4.1 9.6 - - + -
1095A ASN* 2.9 19.5 + - + +
1096A TYR* 3.2 18.2 - - + +
1098A LYS* 1.3 75.9 - - - +
1100A LEU* 1.3 64.6 + - + +
1102A ASN 3.0 9.9 + - - +
1103A ILE* 2.9 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080A ILE* 4.0 19.3 - - + -
1096A TYR* 3.2 48.1 + - + +
1097A LYS* 3.6 8.5 - - - +
1098A LYS 3.3 0.2 - - - -
1099A LEU* 1.3 81.2 - - + +
1101A ASP* 1.3 65.4 + - - +
1102A ASN 3.5 0.2 + - - -
1103A ILE* 3.8 18.5 + - + +
1129A GLU* 3.7 23.6 - - + +
1130A THR* 3.6 32.5 - - - +
1133A ARG* 3.9 34.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097A LYS* 3.5 15.2 - - - +
1098A LYS* 3.3 10.7 + - - +
1099A LEU 3.2 0.6 - - - -
1100A LEU* 1.3 80.8 - - - +
1102A ASN* 1.3 66.9 + - - +
1103A ILE 3.5 4.3 + - - +
1129A GLU* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A TYR* 3.5 23.5 + - - +
1069A LEU* 3.8 13.3 - - + +
1073A ASN* 3.1 17.2 + - - -
1098A LYS* 2.8 26.9 + - - +
1099A LEU 3.0 5.8 + - - +
1101A ASP* 1.3 85.3 - - - +
1103A ILE* 1.3 61.8 + - - +
1104A LYS* 3.7 0.9 + - - +
----------------------------------------------------------
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