Contacts of the helix formed by residues 1117 - 1126 (chain D) in PDB entry 5UH8
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 ASP1117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1039D VAL* 3.6 28.8 - - - +
1040D PRO* 3.9 9.6 - - + +
1043D LYS* 3.8 30.0 + - + +
1044D ALA 4.1 4.6 + - - +
1046D ILE* 4.9 0.6 - - - +
1115D SER 3.8 2.4 + - - -
1116D ALA* 1.3 68.4 - - - +
1118D PRO* 1.3 73.1 - - - +
1119D HIS* 2.9 33.0 + - - +
1120D GLU* 3.0 26.1 + - + +
1121D VAL* 3.1 13.2 + - - +
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Residues in contact with PRO1118 (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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1030D ARG* 5.9 0.2 - - - +
1034D LEU* 4.8 8.7 - - + -
1037D ALA* 5.7 6.5 - - - -
1038D ARG 4.5 5.8 - - - +
1040D PRO* 4.1 14.1 - - + -
1116D ALA 3.1 10.1 - - - +
1117D ASP* 1.3 91.1 - - - +
1119D HIS* 1.3 57.3 + - + +
1121D VAL* 3.1 11.9 + - + -
1122D LEU* 2.8 26.0 + - - +
1130D VAL* 3.2 20.8 - - + +
1133D HIS* 4.3 12.3 - - + +
1134D LEU* 4.3 16.6 - - + -
1207D LEU* 3.8 21.1 - - + -
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Residues in contact with HIS1119 (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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1037D ALA* 3.6 23.3 + - + -
1038D ARG 5.6 0.4 - - - -
1039D VAL* 4.3 18.8 - - + -
1117D ASP* 2.9 18.8 + - - +
1118D PRO* 1.3 79.7 - - + +
1120D GLU* 1.3 60.8 + - + +
1122D LEU* 3.3 11.6 + - - +
1123D ARG* 3.2 22.8 + - - +
1207D LEU* 3.6 51.4 + - + +
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Residues in contact with GLU1120 (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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1043D LYS* 2.8 25.8 + - - -
1045D PRO* 5.5 2.6 - - - +
1046D ILE* 4.0 27.4 + - + +
1048D ASP* 4.8 3.8 - - - +
1077D TYR* 6.1 0.7 - - - -
1117D ASP* 3.0 25.3 + - + +
1119D HIS* 1.3 75.9 - - + +
1121D VAL* 1.3 60.4 + - - +
1123D ARG* 3.1 35.0 + - - +
1124D VAL* 2.8 33.8 + - - +
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Residues in contact with VAL1121 (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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1046D ILE* 3.9 20.4 - - + -
1108D GLY 6.1 0.2 - - - +
1116D ALA* 4.4 12.6 - - + -
1117D ASP 3.1 16.7 + - - +
1118D PRO* 3.1 14.6 + - + +
1120D GLU* 1.3 75.8 - - - +
1122D LEU* 1.3 55.1 + - - +
1125D GLN* 2.7 45.7 + - - +
1126D GLY 3.3 5.7 + - - +
1129D GLU* 4.2 8.7 - - + -
1130D VAL* 3.9 24.9 - - + -
1133D HIS* 4.5 15.9 - - + +
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Residues in contact with LEU1122 (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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1118D PRO 2.8 12.3 + - - +
1119D HIS* 3.3 14.6 - - - +
1120D GLU 3.1 0.2 - - - -
1121D VAL* 1.3 73.8 - - - +
1123D ARG* 1.3 63.5 + - + +
1126D GLY* 2.9 30.3 + - - -
1127D PRO* 3.6 37.4 - - + +
1130D VAL* 4.1 13.8 - - + +
1162D LEU* 4.6 4.3 - - + -
1204D ARG* 6.4 0.2 - - - -
1205D PRO* 3.2 41.0 - - + +
1206D VAL* 3.8 1.8 - - - +
1207D LEU* 3.7 26.9 - - + +
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Residues in contact with ARG1123 (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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1048D ASP* 3.9 24.4 + - - -
1119D HIS 3.2 9.2 + - - +
1120D GLU* 3.1 59.9 + - - +
1122D LEU* 1.3 81.8 - - - +
1124D VAL* 1.3 73.6 + - - +
1126D GLY* 4.9 0.5 + - - -
1204D ARG* 5.7 11.9 - - - +
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Residues in contact with VAL1124 (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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1046D ILE* 4.4 10.1 - - + -
1047D ALA 4.1 8.5 - - - +
1048D ASP* 3.7 41.7 - - + +
1107D VAL* 4.1 14.0 - - + +
1108D GLY* 4.3 3.8 - - - -
1120D GLU 2.8 22.2 + - - +
1121D VAL 4.3 0.2 - - - +
1123D ARG* 1.3 99.3 - - - +
1125D GLN* 1.3 75.7 + - + +
1126D GLY 3.5 0.2 - - - -
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Residues in contact with GLN1125 (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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1046D ILE* 5.3 1.1 - - + +
1107D VAL* 3.5 28.6 + - + +
1108D GLY* 3.7 20.2 - - - +
1121D VAL* 2.7 29.8 + - + +
1124D VAL* 1.3 89.9 - - + +
1126D GLY* 1.3 58.3 + - - +
1129D GLU* 3.5 49.2 + - + +
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Residues in contact with GLY1126 (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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1121D VAL 3.3 1.8 + - - +
1122D LEU* 2.9 20.1 + - - -
1123D ARG 4.7 0.2 - - - -
1124D VAL 3.5 1.4 + - - -
1125D GLN* 1.3 78.9 - - - +
1127D PRO* 1.3 77.1 - - - +
1128D ARG 3.4 2.9 - - - -
1129D GLU 3.3 2.9 + - - -
1130D VAL* 3.2 21.8 + - - +
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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