Contacts of the helix formed by residues 1124 - 1141 (chain A) in PDB entry 5W0N
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 ASN1124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A PHE* 3.7 11.0 - - + -
1062A CYS* 3.6 16.0 - - + +
1104A VAL* 3.9 24.5 - - + +
1121A SER* 3.2 30.0 + - - +
1122A LEU 3.1 2.2 + - - +
1123A TYR* 1.3 72.1 - - - +
1125A THR* 1.3 64.3 + - - +
1126A LEU* 3.4 2.0 + - - +
1127A ALA* 3.1 37.1 + - + +
1128A LEU* 3.4 14.4 + - - +
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Residues in contact with THR1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A CYS* 5.5 0.2 - - - -
1064A THR* 6.0 0.3 - - - +
1069A GLU 5.6 1.2 + - - -
1123A TYR* 3.0 25.0 + - - +
1124A ASN* 1.3 71.6 - - - +
1126A LEU* 1.3 62.4 + - - +
1128A LEU* 3.1 24.9 + - + +
1129A HIS* 3.1 29.3 + - + -
1206A VAL* 3.4 29.4 - - + -
1207A ASP* 4.0 11.4 + - - -
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Residues in contact with LEU1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124A ASN* 3.4 2.4 + - - +
1125A THR* 1.3 76.5 - - - +
1127A ALA* 1.3 61.1 - - - +
1129A HIS* 3.1 6.3 + - - +
1130A ASN* 3.0 27.7 + - - +
1206A VAL* 3.6 23.8 - - + +
1207A ASP* 4.5 14.3 + - + +
1209A TRP* 3.7 27.8 - - + +
1211A ILE* 3.6 29.8 - - + -
1280A ASP* 5.9 0.9 - - - +
1282A PHE* 4.3 13.9 - - + -
1283A ASP* 4.1 23.8 - - + +
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Residues in contact with ALA1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A PHE* 3.5 24.9 - - + -
1124A ASN* 3.1 35.2 + - - +
1125A THR 3.2 0.6 - - - -
1126A LEU* 1.3 77.6 - - - +
1128A LEU* 1.3 61.8 + - - +
1130A ASN* 3.2 15.8 - - - +
1131A THR* 2.8 31.0 + - - -
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Residues in contact with LEU1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A SER* 4.0 21.3 - - - +
1044A LEU 3.7 23.8 - - - +
1045A PHE* 3.8 9.8 - - + +
1062A CYS* 3.9 27.4 - - + -
1064A THR* 5.9 2.0 - - + -
1124A ASN 3.4 9.1 + - - +
1125A THR* 3.1 18.4 + - + +
1127A ALA* 1.3 78.4 - - - +
1129A HIS* 1.3 64.2 + - + +
1131A THR* 3.4 7.0 - - + +
1132A ARG* 3.2 28.2 + - - +
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Residues in contact with HIS1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125A THR* 3.1 34.9 + - + -
1126A LEU* 3.1 8.4 + - - +
1128A LEU* 1.3 77.3 - - + +
1130A ASN* 1.3 60.3 + - - +
1131A THR 3.2 1.3 - - - -
1132A ARG* 3.2 36.1 + - - +
1133A LEU* 2.8 25.6 + - - +
1206A VAL* 3.9 21.9 - - + +
1211A ILE* 3.6 34.8 - - + +
1213A PHE* 4.0 2.9 - - - -
1282A PHE* 3.5 21.1 - - + -
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Residues in contact with ASN1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A PHE* 5.9 0.2 - - - -
1126A LEU* 3.0 21.7 + - - +
1127A ALA* 3.2 19.2 - - - +
1129A HIS* 1.3 74.1 - - - +
1131A THR* 1.3 68.0 + - - +
1133A LEU* 3.7 4.0 - - + -
1134A LEU* 2.9 35.3 + - + +
1171A TYR* 3.3 44.1 + - + +
1280A ASP* 4.1 7.9 + - - +
1281A PRO* 4.5 6.1 - - + -
1282A PHE* 3.4 18.9 - - + -
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Residues in contact with THR1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044A LEU 5.2 0.7 - - - +
1045A PHE* 3.4 8.8 - - - +
1046A GLY* 3.0 34.5 + - - +
1049A LYS* 3.6 32.5 - - + +
1050A ASN* 3.7 13.2 - - - +
1127A ALA 2.8 20.0 + - - -
1128A LEU* 3.4 8.3 - - + +
1130A ASN* 1.3 84.7 + - - +
1132A ARG* 1.3 61.6 + - + +
1134A LEU* 3.4 0.6 + - - -
1135A SER* 2.9 28.4 + - - -
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Residues in contact with ARG1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128A LEU* 3.2 13.9 + - - +
1129A HIS* 3.2 38.7 + - - +
1131A THR* 1.3 79.1 - - + +
1133A LEU* 1.3 64.5 + - - +
1135A SER* 3.3 8.0 + - - -
1136A ALA* 2.9 24.1 + - - +
1211A ILE* 5.2 2.8 - - - +
1213A PHE* 3.4 34.4 + - + -
1215A ASP* 3.4 24.5 + - - +
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Residues in contact with LEU1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129A HIS 2.8 16.0 + - - +
1130A ASN* 3.6 6.7 - - - +
1131A THR 3.2 0.2 - - - -
1132A ARG* 1.3 76.5 - - - +
1134A LEU* 1.3 66.3 + - + +
1136A ALA* 3.2 5.4 + - - +
1137A TYR* 3.1 49.7 + - + +
1192A LEU* 4.4 5.4 - - + -
1193A GLN* 3.8 12.8 - - + +
1213A PHE* 3.6 43.9 - - + -
1258A ILE* 4.0 13.0 - - + -
1281A PRO* 3.7 36.3 - - + -
1282A PHE* 4.2 9.0 - - + -
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Residues in contact with LEU1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050A ASN* 3.6 31.7 - - + +
1052A PHE* 3.8 7.2 - - + -
1130A ASN* 2.9 23.2 + - + +
1131A THR* 5.7 0.2 - - - -
1133A LEU* 1.3 89.9 - - + +
1135A SER* 1.3 57.2 + - - +
1137A TYR* 3.2 8.6 + - - +
1138A SER* 2.9 27.9 + - - -
1171A TYR* 3.8 35.7 - - + +
1174A THR* 3.6 26.0 - - + -
1175A LEU* 4.4 8.5 - - + -
1178A LEU* 4.0 23.1 - - + -
1258A ILE* 4.8 0.2 - - + -
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Residues in contact with SER1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A LYS 3.6 21.6 + - - -
1050A ASN* 3.4 12.6 + - - -
1051A GLY* 4.9 0.9 + - - -
1131A THR 2.9 17.9 + - - -
1132A ARG* 3.5 8.5 - - - -
1133A LEU 3.2 0.2 - - - -
1134A LEU* 1.3 78.0 - - - +
1136A ALA* 1.3 61.1 + - - +
1138A SER* 2.7 21.5 + - - -
1139A ALA* 3.3 9.0 + - - +
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Residues in contact with ALA1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132A ARG 2.9 12.9 + - - +
1133A LEU 3.5 9.0 - - - +
1135A SER* 1.3 75.7 - - - +
1137A TYR* 1.3 62.9 + - - +
1139A ALA* 3.1 15.2 + - - +
1140A ILE* 3.4 16.6 + - - +
1192A LEU* 3.8 17.3 - - + -
1213A PHE* 4.1 13.2 - - + -
1214A PHE 4.7 1.1 - - - +
1215A ASP* 4.8 4.7 - - + +
1217A ILE* 3.9 18.8 - - + +
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Residues in contact with TYR1137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A PHE* 5.4 0.2 - - + -
1133A LEU* 3.1 52.7 + - + +
1134A LEU* 3.2 6.9 + - - +
1136A ALA* 1.3 75.8 - - - +
1138A SER* 1.3 63.3 + - - +
1139A ALA 3.1 1.0 + - - -
1140A ILE* 3.1 31.8 + - + +
1144A VAL* 3.6 15.6 - - + +
1178A LEU* 3.9 32.5 - - + -
1182A GLN* 2.9 25.1 + - - -
1189A ILE* 3.6 19.5 - - + -
1190A PRO 3.2 20.2 - - - -
1191A VAL* 3.7 0.3 - - - -
1192A LEU* 3.0 35.3 + - + +
1193A GLN* 4.5 2.9 + - - -
1258A ILE* 4.0 13.9 + - + -
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Residues in contact with SER1138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050A ASN 3.8 5.9 + - - -
1051A GLY* 4.2 3.1 - - - -
1052A PHE* 3.5 29.2 - - - -
1134A LEU 2.9 8.9 + - - -
1135A SER* 2.7 23.6 + - - -
1137A TYR* 1.3 75.3 - - - +
1139A ALA* 1.3 59.2 + - - +
1141A ASP 3.7 14.1 - - - +
1142A PRO* 5.1 0.9 - - - +
1144A VAL* 3.9 12.1 - - - +
1145A LYS* 3.9 31.9 - - - +
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Residues in contact with ALA1139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135A SER 3.3 8.3 + - - +
1136A ALA* 3.1 12.2 + - - +
1137A TYR 3.1 1.0 - - - -
1138A SER* 1.3 79.9 + - - +
1140A ILE* 1.3 64.8 + - - +
1141A ASP* 3.3 1.9 + - - -
1145A LYS* 5.9 0.4 - - - +
1217A ILE* 4.2 15.8 - - + +
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Residues in contact with ILE1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136A ALA 3.4 11.0 - - - +
1137A TYR* 3.1 35.1 + - + +
1139A ALA* 1.3 80.4 - - - +
1141A ASP* 1.3 62.3 + - + +
1142A PRO* 4.9 0.5 - - - +
1188A VAL 4.5 6.3 - - - +
1189A ILE* 4.1 15.9 - - + -
1190A PRO* 3.8 22.0 - - + -
1192A LEU* 4.1 13.0 - - + -
1217A ILE* 3.9 21.5 - - + -
1220A LEU* 3.8 22.2 - - + -
1224A TRP* 4.5 6.7 - - + -
1227A CYS* 6.0 1.8 - - - -
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Residues in contact with ASP1141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137A TYR 4.2 1.2 + - - -
1138A SER 3.7 8.8 - - - +
1139A ALA 3.3 2.1 - - - -
1140A ILE* 1.3 87.7 - - + +
1142A PRO* 1.3 80.2 - - - +
1143A ARG* 2.9 66.0 + - - +
1144A VAL* 3.0 32.2 + - + +
1145A LYS 4.0 0.3 + - - -
1188A VAL* 4.5 9.1 - - + +
1228A GLY* 6.1 1.0 - - - -
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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) + - + + + + + -
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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