Contacts of the helix formed by residues 1085 - 1098 (chain B) 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 ILE1085 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802B ASN* 6.2 1.3 - - - +
838B SER* 4.5 8.3 - - - +
842B GLU* 3.7 31.9 - - + +
1077B ARG* 5.4 4.7 - - + +
1078B PRO* 4.7 14.4 - - + +
1080B ALA* 3.7 27.6 - - + +
1081B PRO 3.0 11.1 + - - +
1082B PRO* 3.3 24.5 - - + +
1083B PRO 3.2 1.0 - - - -
1084B PHE* 1.3 79.0 - - - +
1086B LEU* 1.3 72.6 + - + +
1087B LEU 3.3 0.4 - - - -
1088B SER* 2.3 40.1 + - - +
1089B HIS* 3.1 20.9 + - + +
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Residues in contact with LEU1086 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834B LEU* 5.4 5.8 - - + +
837B PHE* 4.2 26.0 - - + -
838B SER* 3.6 29.6 - - - -
841B CYS* 4.4 11.7 - - - -
1082B PRO 3.9 2.5 - - - +
1083B PRO* 3.3 21.5 - - + +
1084B PHE 3.3 2.6 - - - -
1085B ILE* 1.3 76.6 - - + +
1087B LEU* 1.3 52.6 + - - +
1089B HIS* 2.9 24.0 - - + +
1090B LEU* 2.8 39.6 + - + +
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Residues in contact with LEU1087 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B PHE* 3.7 25.4 - - + +
1086B LEU* 1.3 76.6 - - - +
1088B SER* 1.3 67.5 + - - +
1090B LEU* 3.1 21.7 + - + +
1091B GLN* 2.6 37.3 + - + +
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Residues in contact with SER1088 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078B PRO* 4.2 20.9 - - - +
1080B ALA* 5.1 6.7 - - - -
1085B ILE* 2.3 38.7 + - - +
1087B LEU* 1.3 87.5 - - - +
1089B HIS* 1.3 52.0 + - - +
1091B GLN* 3.0 9.8 + - - +
1092B LEU* 2.7 36.0 + - - +
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Residues in contact with HIS1089 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B CYS* 3.5 32.5 - - - -
842B GLU* 3.4 34.0 + - - -
845B ARG* 3.9 27.1 - - + +
1078B PRO* 6.1 2.5 - - + -
1085B ILE* 3.1 38.4 + - + +
1086B LEU* 2.9 21.5 + - + +
1088B SER* 1.3 80.6 + - - +
1090B LEU* 1.3 54.7 - - - +
1092B LEU* 3.0 14.9 + - - +
1093B PHE* 2.8 24.7 + - - +
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Residues in contact with LEU1090 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086B LEU* 2.8 15.8 + - + +
1087B LEU* 3.1 29.1 + - + +
1089B HIS* 1.3 71.3 - - - +
1091B GLN* 1.3 64.4 + - + +
1093B PHE* 3.0 14.4 + - + +
1094B ILE* 2.9 38.9 + - + +
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Residues in contact with GLN1091 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087B LEU* 2.6 18.2 + - + +
1088B SER* 3.2 15.0 - - - +
1090B LEU* 1.3 75.7 - - + +
1092B LEU* 1.3 61.4 + - - +
1094B ILE* 3.0 21.1 + - - +
1095B LYS* 3.3 9.7 + - - +
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Residues in contact with LEU1092 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B ARG* 3.8 42.0 - - + +
1078B PRO* 5.4 7.6 - - + -
1088B SER 2.7 15.2 + - - +
1089B HIS* 3.0 14.1 + - - +
1091B GLN* 1.3 72.8 - - - +
1093B PHE* 1.3 60.6 + - + +
1095B LYS* 3.0 14.6 + - + +
1096B ARG* 2.8 27.9 + - + +
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Residues in contact with PHE1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089B HIS 2.8 12.9 + - - +
1090B LEU* 3.0 19.0 + - + +
1092B LEU* 1.3 75.3 - - + +
1094B ILE* 1.3 58.3 + - + +
1096B ARG* 3.0 19.6 + - + +
1097B VAL* 2.6 41.3 + - + +
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Residues in contact with ILE1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090B LEU* 2.9 28.3 + - + +
1091B GLN* 3.0 11.4 + - - +
1093B PHE* 1.3 82.2 - - + +
1095B LYS* 1.3 51.2 + - - +
1097B VAL* 2.9 12.7 + - + +
1098B VAL* 2.7 40.6 + - + +
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Residues in contact with LYS1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091B GLN 3.3 5.9 + - - +
1092B LEU* 3.0 19.2 + - + +
1094B ILE* 1.3 77.8 - - - +
1096B ARG* 1.3 56.9 + - - +
1098B VAL 3.0 23.8 - - - +
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Residues in contact with ARG1096 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B LEU* 2.8 17.6 + - + +
1093B PHE* 3.0 31.6 + - + +
1095B LYS* 1.3 79.1 - - - +
1097B VAL* 1.3 58.6 + - - +
1098B VAL 4.7 0.7 - - - +
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Residues in contact with VAL1097 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B PHE* 2.6 25.8 + - + +
1094B ILE* 2.9 16.8 + - + +
1096B ARG* 1.3 75.7 - - - +
1098B VAL* 1.3 59.9 + - + +
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Residues in contact with VAL1098 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094B ILE* 2.7 20.9 + - + +
1095B LYS* 3.0 22.0 - - - +
1096B ARG 4.6 0.7 - - - +
1097B VAL* 1.3 78.8 - - + +
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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