Contacts of the helix formed by residues 1017 - 1022 (chain A) in PDB entry 2I6W
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 LEU1017 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A ILE* 4.6 12.8 - - + -
907A LEU* 4.0 28.0 - - + +
910A ILE* 4.6 5.4 - - + -
1013A THR* 3.0 34.1 - - - +
1015A THR 3.2 2.4 + - - -
1016A VAL* 1.3 79.1 - - - +
1018A ALA* 1.3 57.4 + - - +
1019A ILE* 2.9 8.9 - - - +
1020A PHE* 2.8 11.5 + - + +
1021A PHE* 2.8 61.3 + - + -
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Residues in contact with ALA1018 (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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904A VAL* 4.4 11.2 - - + -
907A LEU* 3.9 20.7 - - + +
938A SER* 5.7 0.7 - - - +
941A ASN* 5.3 11.9 - - + +
945A ILE* 4.2 3.8 - - - +
1014A ALA 2.9 24.8 + - - +
1015A THR 4.8 0.4 - - - +
1017A LEU* 1.3 78.3 - - - +
1019A ILE* 1.3 57.4 + - - +
1020A PHE 3.2 0.9 - - - -
1022A VAL* 3.0 46.1 + - + +
1023A PRO* 3.8 0.3 - - - +
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Residues in contact with ILE1019 (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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527A TYR* 2.4 65.4 + - + +
531A VAL* 4.5 0.3 - - - +
945A ILE* 4.6 7.4 - - + -
968A VAL* 5.2 0.9 - - + -
971A ARG* 5.3 1.1 - - - -
972A LEU* 3.8 25.8 - - + -
975A ILE* 4.3 26.5 - - + -
976A LEU* 5.8 2.5 - - + -
1015A THR* 2.9 24.3 + - + +
1016A VAL* 3.8 6.5 - - + -
1017A LEU 2.9 11.8 - - - +
1018A ALA* 1.3 80.7 - - - +
1020A PHE* 1.3 73.7 + - + +
1023A PRO* 3.6 9.7 - - - +
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Residues in contact with PHE1020 (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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527A TYR* 3.4 31.9 - + - -
530A SER* 4.3 11.4 - - - -
531A VAL* 4.3 6.4 - - + +
534A ILE* 4.2 28.5 - - + +
541A TYR* 6.2 1.1 - - + -
1016A VAL* 4.7 14.4 - - + -
1017A LEU* 2.8 17.2 + - + +
1019A ILE* 1.3 98.6 - - + +
1021A PHE* 1.3 72.5 + + + +
1023A PRO* 3.2 10.7 - - - +
1024A VAL* 3.1 22.7 - - - +
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Residues in contact with PHE1021 (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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541A TYR* 4.5 22.4 - + + -
544A LEU* 4.1 23.3 - - + -
545A TYR* 3.6 48.2 - + + -
548A ILE* 4.6 8.1 - - + -
907A LEU* 4.5 7.0 - - + -
1017A LEU* 2.8 49.7 + - + +
1020A PHE* 1.3 83.6 - + + +
1022A VAL* 1.3 55.9 + - - +
1024A VAL* 2.6 29.7 + - + -
1025A PHE* 2.7 37.8 + + + -
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Residues in contact with VAL1022 (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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900A SER* 5.9 1.1 - - - -
904A VAL* 3.2 35.0 - - + -
942A ALA* 3.9 20.0 - - + +
945A ILE* 3.4 37.5 - - + -
946A VAL* 4.2 10.5 - - + -
1018A ALA* 3.0 28.3 + - + +
1021A PHE* 1.3 77.5 - - - +
1023A PRO* 1.3 56.0 - - + +
1024A VAL 2.6 11.8 + - - -
1025A PHE* 3.2 12.4 + - + -
1026A PHE* 3.3 21.6 + - + +
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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