Contacts of the helix formed by residues 1150 - 1162 (chain D) in PDB entry 5UHE
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 HIS1150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569D ALA 3.2 19.2 + - - +
570D SER* 4.9 1.9 - - - +
917D GLU 3.3 18.4 + - - -
918D THR* 3.0 26.5 + - - +
920D ALA 4.3 0.6 + - - -
921D TYR* 4.1 3.4 + - + -
922D ALA* 3.4 42.7 + - + +
923D ARG* 4.1 20.0 - - - -
983D MET* 4.4 16.6 - - + -
1148D SER 4.2 0.4 + - - -
1149D ILE* 1.3 75.1 - - - +
1151D ASP* 1.3 65.7 + - - +
1152D LYS* 2.9 37.7 + - + +
1153D HIS* 3.2 22.7 + - + +
1154D ILE* 4.1 2.1 + - - +
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Residues in contact with ASP1151 (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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915D TYR* 5.8 0.3 - - - -
918D THR* 2.8 27.6 + - - +
919D SER* 2.8 24.6 + - - -
923D ARG* 3.6 21.2 + - - +
1135D VAL* 3.7 21.4 - - + +
1136D ARG* 5.7 3.1 - - - +
1139D GLN* 3.4 25.7 - - - +
1150D HIS* 1.3 69.2 - - - +
1152D LYS* 1.3 63.7 + - - +
1154D ILE* 3.0 14.5 + - - +
1155D GLU* 2.9 28.7 + - - +
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Residues in contact with LYS1152 (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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922D ALA* 3.5 14.1 + - - +
923D ARG* 4.7 5.8 - - - +
965D VAL* 4.7 6.0 - - + +
979D TYR* 2.9 70.3 + - + +
981D ARG 2.7 36.1 + - - +
983D MET* 4.6 3.8 - - + -
1150D HIS* 2.9 34.5 + - + +
1151D ASP* 1.3 75.0 - - - +
1153D HIS* 1.3 69.0 + - + +
1155D GLU* 3.1 25.0 + - - +
1156D VAL* 3.1 16.5 + - - +
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Residues in contact with HIS1153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D PRO 2.8 28.7 + - - -
569D ALA* 3.5 18.8 + - - -
979D TYR* 3.4 26.4 + + - -
983D MET* 3.9 11.8 - - + +
998D VAL* 4.7 6.5 - - + -
999D ALA* 3.5 42.8 - - + +
1002D SER* 3.9 11.9 - - - -
1003D ILE* 4.3 3.1 - - + -
1149D ILE* 3.7 15.5 - - + -
1150D HIS* 3.2 18.0 + - + +
1152D LYS* 1.3 74.5 - - + +
1154D ILE* 1.3 66.8 + - - +
1156D VAL* 3.3 9.9 + - - -
1157D ILE* 3.3 16.6 + - - +
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Residues in contact with ILE1154 (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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1003D ILE* 3.8 32.8 - - + -
1035D PHE* 4.4 7.2 - - + -
1135D VAL* 3.9 27.1 - - + +
1138D VAL* 3.6 34.8 - - + -
1139D GLN* 3.8 19.7 - - - +
1142D TYR* 5.4 0.4 - - + -
1149D ILE* 4.6 14.6 - - + -
1150D HIS 4.2 7.4 - - - +
1151D ASP* 3.0 11.8 + - - +
1153D HIS* 1.3 75.3 - - - +
1155D GLU* 1.3 57.6 + - - +
1157D ILE* 3.1 6.1 + - - +
1158D VAL* 2.9 36.8 + - + +
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Residues in contact with GLU1155 (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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897D ILE* 5.2 1.7 - - - +
923D ARG* 2.3 50.7 + - - -
964D SER* 3.0 15.9 + - - +
965D VAL* 4.1 11.5 + - + +
966D LEU* 3.5 26.3 - - + +
1135D VAL* 3.9 19.5 - - + +
1151D ASP* 2.9 22.0 + - - +
1152D LYS* 3.1 11.8 + - - +
1154D ILE* 1.3 74.9 - - - +
1156D VAL* 1.3 60.6 + - - +
1158D VAL* 4.3 3.4 - - - -
1159D ARG* 2.8 33.1 + - - +
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Residues in contact with VAL1156 (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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881D SER* 4.5 3.8 - - - -
884D VAL* 3.6 33.4 - - + -
965D VAL* 4.3 21.5 - - + -
979D TYR* 4.1 24.7 - - + -
995D VAL* 4.3 1.8 - - + +
996D GLY* 3.9 19.3 - - - -
999D ALA* 4.1 7.4 - - + -
1152D LYS 3.1 16.1 + - - +
1153D HIS* 3.3 12.1 + - - +
1155D GLU* 1.3 76.5 - - - +
1157D ILE* 1.3 60.2 + - - +
1159D ARG* 3.6 7.0 - - - +
1160D GLN* 3.3 19.8 - - - +
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Residues in contact with ILE1157 (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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877D LEU* 3.6 24.2 - - + +
880D VAL* 4.2 5.7 - - + +
881D SER* 3.9 25.6 - - - +
999D ALA* 4.4 3.6 - - + -
1000D ALA 4.4 15.9 - - - +
1003D ILE* 3.7 19.1 - - + -
1035D PHE* 3.5 29.6 - - + -
1153D HIS 3.3 16.4 - - - +
1154D ILE 3.1 5.1 + - - +
1156D VAL* 1.3 74.6 - - - +
1158D VAL* 1.3 67.1 + - - +
1160D GLN* 3.0 21.3 + - - +
1161D MET* 3.5 8.2 + - - +
1210D ILE* 4.0 12.3 - - + -
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Residues in contact with VAL1158 (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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966D LEU* 4.5 2.0 - - + -
1035D PHE* 5.0 4.7 - - + -
1131D GLN* 3.6 38.7 + - + +
1134D LEU* 3.9 33.4 - - + -
1135D VAL* 3.8 18.8 - - + -
1138D VAL* 6.0 0.4 - - + -
1154D ILE* 2.9 23.9 + - + +
1155D GLU* 3.8 6.3 - - - +
1157D ILE* 1.3 77.1 - - + +
1159D ARG* 1.3 62.5 - - - +
1161D MET* 2.9 28.3 + - + +
1162D LEU* 3.6 5.6 + - + +
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Residues in contact with ARG1159 (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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884D VAL* 5.2 2.1 - - - +
965D VAL* 3.1 32.6 + - + +
966D LEU* 4.1 18.6 + - + +
968D CYS 3.1 25.5 + - - -
969D ALA* 4.8 2.6 - - - +
970D THR 4.4 6.9 + - - +
973D GLY* 2.8 28.7 + - - -
974D VAL* 3.5 13.3 - - - +
1131D GLN* 4.2 13.4 + - - +
1155D GLU 2.8 18.4 + - - +
1156D VAL* 3.6 6.5 - - - +
1157D ILE 3.1 0.2 - - - -
1158D VAL* 1.3 77.5 - - - +
1160D GLN* 1.3 77.7 + - - +
1161D MET 3.3 0.7 + - - -
1162D LEU* 3.4 12.1 + - - +
1163D ARG* 2.9 42.8 + - + +
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Residues in contact with GLN1160 (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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880D VAL* 3.6 35.6 + - + +
881D SER* 4.4 5.6 - - - -
883D ASP* 5.8 4.6 - - - +
884D VAL* 3.2 30.7 - - + +
1156D VAL 3.3 14.5 - - - +
1157D ILE 3.0 8.4 + - - +
1159D ARG* 1.3 105.3 + - - +
1161D MET* 1.3 61.0 + - - +
1162D LEU 3.3 0.8 + - - -
1163D ARG* 3.4 31.3 + - - +
1164D ARG* 5.2 1.7 + - - -
1208D MET* 4.2 8.5 - - - +
1213D ALA* 4.4 7.9 - - - +
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Residues in contact with MET1161 (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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880D VAL* 5.6 1.3 - - + -
1034D LEU 3.9 8.7 - - - +
1035D PHE* 3.2 40.4 - - - +
1037D ALA* 4.0 14.1 - - + -
1134D LEU* 4.4 13.0 - - + -
1157D ILE 3.7 9.0 - - - +
1158D VAL* 2.9 25.9 + - + +
1160D GLN* 1.3 80.2 - - - +
1162D LEU* 1.3 58.1 + - + +
1163D ARG 3.5 0.4 - - - -
1206D VAL 3.9 1.2 - - - +
1207D LEU* 4.0 15.5 - - + -
1208D MET* 3.0 66.9 + - - +
1209D GLY 4.9 0.2 - - - -
1210D ILE* 4.1 17.9 - - + +
1213D ALA* 5.1 2.2 - - - -
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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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1122D LEU* 4.8 5.6 - - + -
1127D PRO* 3.7 24.5 - - + +
1130D VAL* 3.7 12.8 - - + -
1131D GLN* 3.4 46.0 - - + +
1158D VAL* 3.6 5.1 + - + +
1159D ARG 3.4 5.3 + - - +
1160D GLN 3.3 0.4 - - - -
1161D MET* 1.3 77.9 - - - +
1163D ARG* 1.3 58.3 + - - +
1164D ARG 3.2 11.3 + - - +
1165D VAL* 5.6 0.2 - - - +
1183D ARG* 3.9 15.6 + - - -
1205D PRO* 6.2 1.3 - - + -
1206D VAL 3.8 8.7 - - - +
1207D LEU* 3.6 46.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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