Contacts of the helix formed by residues 1143 - 1165 (chain D) in PDB entry 6PUO
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 ARG1143 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139D GLN 4.0 6.9 + - - +
1140D GLN* 3.1 49.8 + - - +
1141D LYS 3.2 3.4 - - - +
1142D GLN* 1.3 81.6 - - - +
1144D PRO* 1.3 73.7 - - + +
1145D GLU* 3.3 9.5 - - + +
1146D GLN* 3.4 25.4 + - + +
1147D LYS* 3.1 19.8 + - - +
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Residues in contact with PRO1144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145C GLU* 5.9 9.0 - - + -
1148C ILE* 5.3 10.3 - - + +
1142D GLN 4.0 4.0 - - - +
1143D ARG* 1.3 86.2 - - + +
1145D GLU* 1.3 62.0 + - + +
1147D LYS* 3.1 11.0 + - + +
1148D ILE* 2.9 39.4 + - + +
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Residues in contact with GLU1145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144A PRO* 5.9 9.0 - - + -
1147A LYS* 5.6 1.4 - - - +
1143D ARG* 3.3 9.1 - - + +
1144D PRO* 1.3 79.8 - - + +
1146D GLN* 1.3 57.9 + - - +
1148D ILE* 3.3 10.9 + - - +
1149D GLU* 3.0 27.7 + - - +
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Residues in contact with GLN1146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1140D GLN 4.4 9.2 - - - +
1141D LYS* 3.9 24.1 - - - +
1143D ARG* 3.4 34.0 + - + +
1144D PRO 3.3 0.4 - - - -
1145D GLU* 1.3 78.3 - - - +
1147D LYS* 1.3 59.6 + - - +
1149D GLU* 3.3 9.0 + - + +
1150D ASP* 2.9 37.1 + - - +
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Residues in contact with LYS1147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145C GLU 5.6 1.1 - - - +
1148C ILE* 4.2 17.7 - - + +
1149C GLU* 4.7 19.5 - - + -
1152C SER* 4.8 8.0 + - - +
1141D LYS* 4.6 10.0 + - - +
1142D GLN* 4.0 29.8 + - - +
1143D ARG 3.1 15.7 + - - +
1144D PRO* 3.1 12.3 + - + +
1146D GLN* 1.3 77.1 + - - +
1148D ILE* 1.3 59.6 + - - +
1150D ASP* 3.4 5.6 + - + +
1151D ILE* 2.9 47.6 + - + +
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Residues in contact with ILE1148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144A PRO* 5.3 11.0 - - + +
1147A LYS* 4.2 17.9 - - + -
1148A ILE* 4.4 28.5 - - + -
1151A ILE* 3.9 20.5 - - + +
1148C ILE* 4.5 28.7 - - + -
1144D PRO* 2.9 24.2 + - + +
1145D GLU* 3.7 8.3 - - - +
1147D LYS* 1.3 75.7 - - - +
1149D GLU* 1.3 58.6 + - - +
1151D ILE* 3.3 9.5 + - + +
1152D SER* 2.9 27.9 + - - -
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Residues in contact with GLU1149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147A LYS* 4.7 14.1 - - + +
1145D GLU 3.0 17.0 + - - +
1146D GLN* 3.6 13.5 - - + +
1147D LYS 3.3 0.2 - - - -
1148D ILE* 1.3 77.6 - - - +
1150D ASP* 1.3 56.1 + - - +
1152D SER* 3.3 6.1 + - - +
1153D ASN* 2.9 41.0 + - - +
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Residues in contact with ASP1150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146D GLN* 2.9 28.5 + - - +
1147D LYS* 3.8 6.5 - - + +
1149D GLU* 1.3 76.1 - - - +
1151D ILE* 1.3 58.5 + - + +
1153D ASN* 3.3 10.6 + - - +
1154D LYS* 3.0 34.5 + - - +
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Residues in contact with ILE1151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151A ILE* 5.1 15.8 - - + +
1148C ILE* 3.9 26.9 - - + +
1151C ILE* 5.1 13.9 - - + -
1152C SER* 3.7 38.6 - - - +
1155C VAL* 5.4 11.1 - - + +
1147D LYS* 2.9 29.0 + - + +
1148D ILE* 3.3 8.7 + - + +
1150D ASP* 1.3 76.9 - - + +
1152D SER* 1.3 62.5 + - - +
1154D LYS* 3.4 16.8 + - - +
1155D VAL* 3.4 15.8 + - + +
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Residues in contact with SER1152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147A LYS* 4.8 11.7 + - - +
1151A ILE* 3.6 29.0 - - - +
1154A LYS* 4.5 8.8 + - - -
1148D ILE 2.9 17.6 + - - -
1149D GLU* 3.7 7.0 - - - -
1151D ILE* 1.3 75.3 - - - +
1153D ASN* 1.3 67.9 + - - +
1155D VAL* 3.3 20.2 - - - +
1156D ASP* 3.4 11.3 + - - +
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Residues in contact with ASN1153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1149D GLU* 2.9 29.5 + - - +
1150D ASP* 3.3 8.5 + - - +
1152D SER* 1.3 81.0 + - - +
1154D LYS* 1.3 62.9 + - - +
1155D VAL 3.5 0.2 + - - -
1156D ASP* 3.6 21.3 + - - +
1157D ALA* 4.1 4.3 + - - +
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Residues in contact with LYS1154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152C SER* 4.4 9.9 + - - -
1155C VAL* 3.7 22.9 - - + +
1156C ASP* 2.4 42.0 + - - +
1159C VAL* 4.0 21.9 - - + +
1150D ASP* 3.0 21.3 + - - +
1151D ILE* 3.8 8.0 - - - +
1152D SER 3.2 0.6 - - - -
1153D ASN* 1.3 79.4 - - - +
1155D VAL* 1.3 60.9 + - - +
1156D ASP 3.3 0.3 + - - -
1157D ALA* 3.5 15.5 + - + +
1158D MET* 3.7 11.0 - - - +
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Residues in contact with VAL1155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A ILE* 5.4 12.1 - - + +
1154A LYS* 3.7 26.9 - - + +
1155A VAL* 5.4 12.3 - - + -
1158A MET* 4.0 20.6 - - - -
1155C VAL* 5.4 9.8 - - + +
1151D ILE* 3.4 11.0 + - + +
1152D SER* 3.3 17.7 - - - +
1154D LYS* 1.3 76.5 - - - +
1156D ASP* 1.3 61.1 + - - +
1158D MET* 3.2 14.5 + - + +
1159D VAL* 2.9 27.9 + - + +
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Residues in contact with ASP1156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154A LYS* 2.4 40.1 + - - +
1152D SER* 3.4 14.1 + - - +
1153D ASN* 3.8 15.2 - - - +
1154D LYS 3.2 0.8 - - - -
1155D VAL* 1.3 76.4 - - - +
1157D ALA* 1.3 60.0 + - - +
1159D VAL* 3.2 8.2 + - + +
1160D ASP* 2.9 29.5 + - - +
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Residues in contact with ALA1157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159C VAL* 6.2 1.6 - - + -
1153D ASN 4.1 3.9 + - - +
1154D LYS* 3.5 13.4 + - + +
1155D VAL 3.3 0.6 - - - -
1156D ASP* 1.3 79.3 - - - +
1158D MET* 1.3 56.8 + - + +
1160D ASP* 3.4 5.8 + - - +
1161D LEU* 2.9 35.2 + - + +
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Residues in contact with MET1158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158A MET* 3.8 21.7 - - + +
1162B LEU* 5.6 1.1 - - + -
1155C VAL* 4.0 21.5 - - - -
1158C MET* 3.8 42.8 - - + +
1159C VAL* 3.7 26.0 - - + +
1162C LEU* 4.0 25.2 - - + +
1154D LYS 3.7 14.4 - - - +
1155D VAL* 3.2 12.0 + - - +
1157D ALA* 1.3 73.5 - - + +
1159D VAL* 1.3 60.6 + - - +
1161D LEU* 3.9 1.6 - - - +
1162D LEU* 2.9 32.7 + - - +
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Residues in contact with VAL1159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154A LYS* 4.0 27.8 - - + +
1157A ALA* 6.1 2.2 - - + -
1158A MET* 3.7 27.8 - - + -
1161A LEU* 5.6 0.7 - - - +
1155D VAL* 2.9 17.4 + - + +
1156D ASP* 3.2 11.9 + - - +
1158D MET* 1.3 76.7 - - - +
1160D ASP* 1.3 59.3 + - + +
1162D LEU* 3.8 2.5 - - - +
1163D ASP* 2.9 33.4 + - + +
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Residues in contact with ASP1160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156D ASP 2.9 15.9 + - - +
1157D ALA* 3.9 5.2 - - - +
1159D VAL* 1.3 79.3 - - + +
1161D LEU* 1.3 57.0 + - - +
1163D ASP* 3.8 4.2 - - - +
1164D LEU* 2.9 34.4 + - - +
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Residues in contact with LEU1161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159C VAL 5.6 0.7 - - - +
1162C LEU* 3.7 53.4 - - + +
1163C ASP* 4.6 9.4 - - + -
1157D ALA* 2.9 20.9 + - + +
1158D MET* 5.4 0.2 - - - -
1160D ASP* 1.3 77.2 - - - +
1162D LEU* 1.3 61.3 + - - +
1164D LEU* 4.4 3.4 - - - +
1165D ASP* 3.7 23.4 + - + +
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Residues in contact with LEU1162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158A MET* 4.0 33.2 - - + +
1161A LEU* 3.7 50.4 - - + +
1162A LEU* 4.5 22.0 - - + +
1158B MET* 5.6 1.1 - - + -
1162C LEU* 4.5 22.1 - - + +
1158D MET 2.9 18.5 + - - +
1159D VAL* 3.9 3.1 - - - +
1161D LEU* 1.3 77.1 - - - +
1163D ASP* 1.3 61.0 + - - +
1164D LEU 3.4 0.2 - - - -
1165D ASP* 4.3 8.4 + - - +
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Residues in contact with ASP1163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A LEU* 4.5 12.8 - - + +
1159D VAL* 2.9 21.1 + - + +
1160D ASP* 4.0 4.9 - - - +
1161D LEU 3.3 0.2 - - - -
1162D LEU* 1.3 78.9 - - - +
1164D LEU* 1.3 62.7 + - - +
1165D ASP 3.5 2.4 - - - -
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Residues in contact with LEU1164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D GLY 5.6 2.3 - - - +
1160D ASP 2.9 17.8 + - - +
1161D LEU* 4.4 4.5 - - - +
1162D LEU 3.4 0.4 - - - -
1163D ASP* 1.3 78.0 - - - +
1165D ASP* 1.3 64.2 + - - +
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Residues in contact with ASP1165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161D LEU* 3.7 17.6 + - + +
1162D LEU 4.3 6.2 + - - +
1163D ASP 3.5 3.9 - - - -
1164D LEU* 1.3 83.0 - - - +
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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