Contacts of the helix formed by residues 1089 - 1103 (chain N) in PDB entry 2A69
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 ALA1089 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085N ALA 4.5 2.9 + - - +
1086N LEU 4.0 7.3 + - - +
1087N ARG 2.8 0.2 - - - -
1088N THR* 1.3 80.3 - - - +
1090N ASP* 1.3 61.4 + - - +
1091N SER 3.7 1.6 - - - -
1092N GLY 4.5 1.6 - - - -
1093N TYR* 3.5 20.0 + - - +
9221N MG 3.8 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1090 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086N LEU* 3.4 21.5 + - - +
1087N ARG* 3.0 20.4 + - + -
1089N ALA* 1.3 82.1 - - - +
1091N SER* 1.4 54.0 + - - +
1092N GLY 3.3 5.6 - - - -
1093N TYR* 2.9 39.2 + - - +
1094N LEU* 3.4 8.3 + - - +
1238N MET* 4.9 4.0 - - - +
1241N PHE* 3.1 38.0 - - - -
1256N LEU* 4.3 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1091 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706N PRO* 5.7 2.1 - - - +
708N LEU* 4.1 18.9 - - - +
1087N ARG* 2.9 24.3 + - - +
1088N THR* 4.5 7.8 + - - -
1090N ASP* 1.4 66.6 - - - +
1092N GLY* 1.3 56.2 + - - +
1094N LEU* 4.3 2.7 + - - +
1095N THR* 2.8 27.4 + - - -
1230N GLY* 3.3 15.7 - - - +
1233N GLY 5.5 1.6 - - - -
1234N THR* 3.1 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1092 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035M MET* 5.1 15.0 - - - -
1038M TRP* 6.0 0.7 - - - -
708N LEU* 5.8 1.6 - - - -
1089N ALA 4.3 2.4 + - - -
1090N ASP 3.3 0.2 - - - -
1091N SER* 1.3 79.3 + - - +
1093N TYR* 1.3 66.8 + - - +
1094N LEU 3.1 2.5 - - - -
1095N THR* 3.1 6.5 + - - -
1096N ARG* 2.8 33.8 + - - -
9221N MG 4.0 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1093 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089N ALA 3.5 10.6 + - - +
1090N ASP* 2.9 42.7 - - - +
1092N GLY* 1.3 76.4 - - - +
1094N LEU* 1.3 69.9 + - + +
1096N ARG* 3.5 14.1 - - - +
1097N LYS* 3.3 43.3 + - + +
1241N PHE* 3.5 32.5 - + - -
1256N LEU* 6.0 1.3 - - + -
1260N ILE* 3.9 27.0 - - + +
1266N ARG* 6.0 0.2 + - - -
9221N MG 4.1 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1094 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090N ASP 3.4 8.2 + - - +
1091N SER* 4.4 5.6 - - - +
1092N GLY 3.1 0.4 - - - -
1093N TYR* 1.3 80.1 - - + +
1095N THR* 1.3 59.1 + - - +
1096N ARG 2.7 13.4 + - - -
1097N LYS* 2.8 19.9 + - + +
1098N LEU* 3.1 36.6 + - + +
1229N ILE* 4.4 9.9 - - + +
1230N GLY* 4.9 4.7 - - - +
1233N GLY* 5.1 9.2 - - - -
1236N LEU* 6.1 0.4 - - + -
1256N LEU* 4.3 18.2 - - + -
1259N VAL* 4.9 15.7 - - + +
1260N ILE* 3.6 27.4 - - + -
1263N PHE* 5.1 7.6 - - + -
1356N TYR* 4.2 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1095 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035M MET* 6.2 1.3 - - + -
1038M TRP* 4.4 16.8 - - + -
708N LEU* 5.1 8.2 + - - +
1091N SER 2.8 21.1 + - - -
1092N GLY* 3.1 7.0 + - - -
1094N LEU* 1.3 75.8 - - - +
1096N ARG* 1.3 56.6 + - - +
1098N LEU* 4.4 4.0 - - - -
1099N VAL* 2.8 44.0 + - + +
1226N ALA 3.1 33.2 - - - +
1227N GLN* 4.0 13.5 - - + -
1230N GLY* 3.6 12.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1096 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034M GLU* 2.7 28.7 + - - +
1035M MET* 4.5 5.6 - - - +
1038M TRP* 3.5 27.1 - - + -
1092N GLY* 2.8 26.8 + - - +
1093N TYR* 3.5 10.5 - - - +
1094N LEU 2.7 4.0 + - - -
1095N THR* 1.3 72.6 - - - +
1097N LYS* 1.3 53.2 + - + +
1099N VAL* 3.0 4.2 + - - +
1100N ASP* 2.7 50.0 + - - +
1440N PHE* 6.1 2.7 - - + -
9221N MG 3.4 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1097 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093N TYR* 3.3 48.9 + - + +
1094N LEU* 2.8 15.0 + - + +
1096N ARG* 1.3 72.9 - - + +
1098N LEU* 1.3 67.8 + - + +
1100N ASP* 2.9 23.5 + - - +
1101N VAL* 3.0 20.3 + - - +
1260N ILE* 5.7 1.5 - - + +
1264N GLU* 4.1 20.7 + - - +
1424N VAL* 4.2 17.3 - - + -
1425N THR* 4.1 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1098 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094N LEU* 3.1 46.5 + - + +
1095N THR* 3.8 4.7 - - - +
1097N LYS* 1.3 82.6 - - + +
1099N VAL* 1.3 57.4 + - - +
1101N VAL* 3.2 3.7 + - - -
1102N THR* 2.3 40.5 + - - +
1226N ALA* 3.4 37.5 - - + +
1229N ILE* 3.5 36.8 - - + -
1230N GLY 4.7 2.2 - - - +
1263N PHE* 4.8 11.9 - - + -
1371N VAL* 4.4 13.5 - - + -
1424N VAL* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1099 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038M TRP* 3.6 45.1 - - + +
1041M GLU* 5.5 0.2 - - - +
1095N THR* 2.8 36.8 + - + +
1096N ARG 3.7 2.5 - - - +
1098N LEU* 1.3 69.5 - - - +
1100N ASP* 1.3 66.7 + - - +
1101N VAL 3.2 0.2 - - - -
1102N THR 3.8 1.3 - - - +
1103N HIS* 3.1 39.1 + - + +
1223N ILE* 4.4 15.9 - - + -
1226N ALA* 3.5 22.2 - - + -
1227N GLN* 5.6 0.2 - - + -
1463N LYS* 4.8 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1100 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038M TRP* 5.4 3.1 - - - -
1096N ARG* 2.7 45.1 + - - +
1097N LYS* 2.9 19.9 + - - +
1099N VAL* 1.3 75.8 - - - +
1101N VAL* 1.3 58.2 + - - +
1103N HIS* 3.2 23.1 + - - -
1104N GLU* 4.6 1.0 - - - +
1428N ALA* 3.7 22.6 - - + +
1431N THR* 5.9 1.6 - - - +
1440N PHE* 3.2 49.7 - - + +
1463N LYS* 5.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1101 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097N LYS* 3.0 17.2 + - - +
1098N LEU 3.9 2.2 - - - +
1100N ASP* 1.3 77.6 - - - +
1102N THR* 1.3 58.2 + - - +
1103N HIS 3.6 0.4 - - - -
1104N GLU* 2.6 29.3 - - - +
1371N VAL* 5.6 0.7 - - + -
1374N GLN* 3.8 23.7 - - + +
1378N TYR* 5.6 0.4 - - - +
1424N VAL* 3.0 44.6 - - + +
1427N SER* 3.2 33.4 - - - +
1428N ALA* 3.7 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1102 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098N LEU* 2.3 31.1 + - - +
1099N VAL* 4.4 1.3 - - - -
1101N VAL* 1.3 81.1 - - - +
1103N HIS* 1.3 64.5 + - - +
1104N GLU 3.4 2.5 - - - -
1105N ILE* 3.1 18.3 - - + +
1222N GLY* 2.9 48.3 - - - +
1225N ALA* 4.8 2.2 - - + -
1226N ALA* 4.4 2.0 - - + -
1370N ILE* 4.0 21.3 - - + +
1371N VAL* 4.2 16.8 - - + +
1374N GLN* 4.9 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1103 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041M GLU* 5.3 0.9 - - - +
1099N VAL* 3.1 32.4 + - + +
1100N ASP* 3.2 25.0 + - - -
1101N VAL 3.6 0.2 - - - -
1102N THR* 1.3 77.4 - - - +
1104N GLU* 1.3 88.3 + - - +
1105N ILE 3.0 8.7 + - - +
1106N VAL* 4.2 1.6 - - - +
1223N ILE* 3.9 19.7 - - + +
1431N THR* 6.5 0.9 - - + -
1432N LYS* 4.8 0.9 - - - -
1436N SER* 4.0 13.9 + - - -
1440N PHE* 6.0 1.3 - + - -
1461N GLY* 3.5 1.9 - - - -
1462N LEU* 3.0 43.9 - - + +
1463N LYS* 3.1 34.0 + - + +
1464N GLU* 3.6 17.5 + - - -
----------------------------------------------------------
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