Contacts of the helix formed by residues 1157 - 1174 (chain A) in PDB entry 5A9U
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 SER1157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155A VAL 4.1 0.2 + - - -
1156A TYR* 1.3 78.1 - - - +
1158A GLU* 1.3 62.3 + - - +
1159A GLN* 3.6 10.8 + - - +
1160A ASP* 3.2 21.2 + - - -
1161A GLU* 3.2 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A SER* 1.3 75.3 - - - +
1159A GLN* 1.3 65.8 + - - +
1161A GLU* 3.2 10.9 + - + +
1162A LEU* 3.0 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A SER* 3.4 8.1 + - - +
1158A GLU* 1.3 75.4 - - - +
1160A ASP* 1.3 64.2 + - - +
1162A LEU* 3.3 18.1 + - - +
1163A ASP* 2.9 51.6 + - - +
1279A ARG* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152A LEU* 4.1 3.3 - - - +
1156A TYR* 3.3 43.5 - - + +
1157A SER* 3.2 28.0 + - - +
1158A GLU 3.3 0.4 - - - -
1159A GLN* 1.3 82.2 - - - +
1161A GLU* 1.3 57.1 + - - +
1163A ASP* 3.6 8.7 - - - +
1164A PHE* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152A LEU* 3.5 24.9 - - + +
1156A TYR* 5.3 2.7 - - + +
1157A SER 3.2 15.3 + - - +
1158A GLU* 3.3 13.9 - - + +
1159A GLN 3.2 0.2 - - - -
1160A ASP* 1.3 79.1 - - - +
1162A LEU* 1.3 59.8 + - + +
1164A PHE* 3.3 4.7 + - - +
1165A LEU* 2.9 29.4 + - - +
1190A LEU* 4.7 4.2 - - - +
1192A ARG* 3.1 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A PRO* 4.0 33.0 - - + +
1158A GLU* 3.0 22.3 + - + +
1159A GLN* 3.3 23.8 + - - +
1161A GLU* 1.3 77.9 - - + +
1163A ASP* 1.3 60.4 + - - +
1165A LEU* 3.2 13.3 + - + +
1166A MET* 2.8 32.8 + - - +
1279A ARG 5.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159A GLN* 2.9 42.9 + - - +
1160A ASP* 3.6 10.1 - - - +
1162A LEU* 1.3 76.4 - - - +
1164A PHE* 1.3 60.7 + - - +
1166A MET* 3.3 1.1 + - - -
1167A GLU 3.0 15.8 + - - -
1275A ARG* 2.6 52.5 + - - +
1276A ASP* 3.6 7.8 - - - +
1279A ARG* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150A LYS* 3.5 38.1 - - + -
1151A THR 3.7 8.5 - - - -
1152A LEU* 3.6 41.5 - - + -
1160A ASP 2.9 17.5 + - - +
1161A GLU 3.3 5.6 - - - +
1163A ASP* 1.3 75.7 - - - +
1165A LEU* 1.3 67.7 + - + +
1167A GLU* 3.3 5.8 + - - +
1168A ALA 3.3 15.2 + - - -
1187A LEU* 4.6 7.0 - - + -
1192A ARG* 3.6 34.8 - - + -
1193A PHE 4.2 1.8 - - - -
1194A ILE* 3.4 43.9 - - + +
1275A ARG* 3.6 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093A ASN* 5.3 1.1 - - + -
1094A PRO* 4.6 12.3 - - + -
1105A ILE* 3.1 48.2 - - + -
1108A LEU* 3.6 13.2 - - + -
1161A GLU* 2.9 13.5 + - - +
1162A LEU* 3.4 17.0 - - + +
1164A PHE* 1.3 82.1 - - + +
1166A MET* 1.3 64.0 + - + +
1168A ALA* 3.1 12.1 + - + +
1169A LEU* 2.8 36.5 - - + +
1187A LEU* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A PRO* 3.8 29.8 - - + -
1095A ASN 4.0 7.9 - - - +
1096A TYR* 3.9 20.2 - - - -
1162A LEU 2.8 19.1 + - - +
1163A ASP* 3.3 1.1 + - - -
1165A LEU* 1.3 75.6 - - + +
1167A GLU* 1.3 56.6 + - - +
1169A LEU* 3.2 16.5 + - + +
1170A ILE* 2.9 42.0 + - + +
1275A ARG* 3.7 22.9 - - + +
1278A TYR* 3.7 32.8 - - + -
1279A ARG 4.4 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150A LYS* 2.8 36.9 + - - +
1163A ASP 3.0 12.1 + - - +
1164A PHE* 3.5 11.7 - - - +
1165A LEU 3.2 0.2 - - - -
1166A MET* 1.3 76.9 - - - +
1168A ALA* 1.3 62.3 + - - +
1170A ILE* 3.4 6.3 + - - +
1171A ILE* 3.1 43.8 + - + +
1194A ILE* 4.7 3.7 - - + +
1270A ASP* 4.5 4.9 - - - +
1271A PHE* 4.3 20.1 + - + +
1272A GLY* 2.9 33.2 + - - -
1275A ARG* 3.6 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108A LEU* 3.8 11.4 - - + -
1164A PHE* 3.3 3.5 + - + +
1165A LEU* 3.1 13.1 + - + +
1167A GLU* 1.3 77.7 - - - +
1169A LEU* 1.3 63.6 + - - +
1171A ILE* 4.1 2.9 - - - +
1172A SER* 2.8 31.1 + - - +
1182A CYS* 4.6 1.5 - - - -
1185A VAL* 4.0 19.3 - - + -
1187A LEU* 5.9 1.1 - - + -
1194A ILE* 3.6 34.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A PRO 4.0 16.6 - - - +
1096A TYR* 4.2 23.1 - - + -
1103A SER* 4.7 6.5 - - - +
1104A SER 4.5 10.1 - - - +
1105A ILE* 4.4 11.9 - - + +
1108A LEU* 3.2 37.2 - - + -
1165A LEU* 2.8 33.6 + - + +
1166A MET* 3.2 33.2 + - + +
1168A ALA* 1.3 76.2 - - - +
1170A ILE* 1.3 63.8 + - - +
1172A SER* 3.3 2.5 + - - -
1173A LYS* 3.3 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A TYR* 3.8 32.1 - - + +
1166A MET* 2.9 28.9 + - + +
1167A GLU* 3.7 6.7 - - - +
1168A ALA 3.3 0.2 - - - -
1169A LEU* 1.3 78.4 - - - +
1171A ILE* 1.3 65.0 + - - +
1173A LYS* 3.3 9.5 + - - +
1174A PHE* 3.4 39.3 + - + -
1245A PHE* 3.9 18.2 - - + -
1271A PHE* 4.2 15.7 - - + +
1274A ALA 4.7 4.3 - - - +
1275A ARG* 3.9 35.2 - - + +
1278A TYR* 5.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150A LYS* 6.2 2.0 - - + -
1167A GLU* 3.1 30.9 + - + +
1168A ALA* 4.2 3.4 - - - +
1170A ILE* 1.3 75.5 - - - +
1172A SER* 1.3 63.4 + - - +
1173A LYS 3.2 1.0 + - - -
1174A PHE* 3.2 27.5 + - + +
1179A ILE* 5.1 0.9 - - + -
1180A VAL* 3.4 37.5 - - + +
1181A ARG* 5.7 0.2 - - - -
1182A CYS* 3.9 21.8 + - + +
1194A ILE* 5.6 3.1 - - + -
1196A LEU* 4.1 21.1 - - + -
1269A GLY 4.7 7.2 - - - +
1270A ASP* 5.6 0.2 - - - -
1271A PHE* 3.9 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108A LEU* 3.4 20.0 - - - +
1109A LYS 5.8 0.2 + - - -
1168A ALA 2.8 21.8 + - - -
1169A LEU* 3.7 4.9 - - - -
1170A ILE 3.2 0.2 - - - -
1171A ILE* 1.3 77.5 - - - +
1173A LYS* 1.3 68.6 + - - +
1174A PHE 3.7 5.4 + - - +
1182A CYS* 3.3 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A TYR* 4.1 11.4 - - + -
1098A PHE* 3.6 34.5 - - + -
1101A LYS* 4.1 33.2 - - - +
1103A SER* 3.9 26.9 - - - +
1107A ASP* 6.1 4.1 - - + +
1169A LEU* 3.3 18.3 + - - +
1170A ILE 3.3 4.9 + - - +
1171A ILE 3.1 1.0 - - - -
1172A SER* 1.3 85.5 + - - +
1174A PHE* 1.3 64.0 + - - +
1175A ASN* 3.8 2.1 + - - +
1239A TYR* 4.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A TYR* 4.7 0.7 - - - -
1098A PHE* 3.6 35.0 - + - -
1170A ILE* 3.4 39.5 - - + -
1171A ILE* 3.2 17.3 + - - +
1172A SER 3.9 7.3 - - - +
1173A LYS* 1.3 81.8 - - - +
1175A ASN* 1.3 61.3 + - - +
1176A HIS 4.1 0.7 - - - +
1179A ILE* 3.7 31.6 - - + -
1181A ARG* 4.5 5.2 + - - -
1239A TYR* 3.6 14.4 - + + +
1240A LEU* 3.5 25.4 - - + -
1245A PHE* 3.8 14.6 - + - -
1271A PHE* 3.4 24.5 - + - -
----------------------------------------------------------
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