Contacts of the helix formed by residues 1024 - 1033 (chain A) in PDB entry 1IWG
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 VAL1024 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900A SER* 4.9 2.2 - - - -
904A VAL* 3.5 17.5 - - + -
907A LEU* 3.3 18.4 - - + -
941A ASN* 5.3 0.2 - - + -
942A ALA* 3.5 25.6 - - - +
945A ILE* 3.0 50.0 - - + +
946A VAL* 5.6 0.2 - - - +
1018A ALA* 3.3 37.5 - - + +
1023A PRO* 1.3 81.0 - - + +
1025A PHE* 1.3 57.0 + - - +
1027A VAL* 3.4 19.7 - - - +
1028A VAL* 5.2 1.1 - - - +
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Residues in contact with PHE1025 (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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531A VAL* 3.4 19.1 - - + -
534A ILE* 5.3 0.7 - - + -
535A LEU* 3.7 19.1 - - + -
945A ILE* 3.4 21.8 - - + -
964A THR* 3.0 55.6 - - + +
965A LEU* 3.8 0.9 - - - -
967A ALA* 5.0 0.2 - - + -
968A VAL* 3.3 37.2 - - + -
971A ARG* 3.7 2.0 - - - -
1018A ALA 5.7 0.2 - - - +
1019A ILE 4.7 10.8 - - - -
1020A PHE 5.0 4.0 - - - +
1021A PHE 5.3 0.2 - - - +
1023A PRO 2.6 7.1 - - - +
1024A VAL* 1.3 86.4 - - - +
1026A PHE* 1.3 68.2 + - + +
1027A VAL* 2.7 12.8 + - - +
1028A VAL* 3.2 6.5 + - + +
1029A VAL* 3.0 27.3 + - - +
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Residues in contact with PHE1026 (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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534A ILE* 3.0 65.7 - - + -
535A LEU* 4.7 5.4 - - + -
537A SER 3.5 11.7 - - - -
538A THR* 4.1 2.6 - - + +
541A TYR* 3.5 36.3 - + + -
1021A PHE 3.6 11.7 - - - -
1023A PRO* 3.7 25.5 - - + -
1025A PHE* 1.3 80.6 - - + +
1027A VAL* 1.3 55.4 + - - +
1029A VAL* 3.5 10.1 - - - +
1030A ARG* 2.8 69.1 + - - +
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Residues in contact with VAL1027 (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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899A PHE 4.8 0.2 - - - +
900A SER* 2.9 46.2 - - - +
903A LEU* 3.3 34.3 - - + -
1023A PRO* 3.4 12.6 - - + -
1024A VAL* 3.4 10.5 - - - +
1025A PHE* 2.7 21.2 - - - +
1026A PHE* 1.3 73.6 - - - +
1028A VAL* 1.3 75.8 + - + +
1029A VAL 2.6 6.1 + - - -
1030A ARG* 3.0 4.3 + - - +
1031A ARG* 2.8 36.6 + - + +
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Residues in contact with VAL1028 (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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896A SER 6.5 0.4 - - - -
897A ILE* 6.3 0.2 - - - -
900A SER* 3.6 10.3 + - - +
945A ILE 4.1 7.4 - - - +
946A VAL* 3.5 33.9 - - + -
950A LYS* 2.7 35.0 - - - +
953A MET* 4.8 4.7 - - + -
964A THR* 4.3 16.4 - - + -
1024A VAL 5.2 0.2 - - - +
1025A PHE* 3.2 9.8 + - + +
1027A VAL* 1.3 86.0 - - + +
1029A VAL* 1.3 56.5 + - - +
1031A ARG* 4.5 1.8 - - - -
1032A ARG* 2.9 48.3 + - + +
1033A PHE* 3.8 3.0 + - + -
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Residues in contact with VAL1029 (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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535A LEU* 4.9 16.2 - - + +
538A THR* 5.3 10.8 - - + +
960A LEU* 4.7 10.5 - - + +
961A ILE* 4.0 31.4 - - + -
964A THR* 4.7 9.9 - - + -
1025A PHE 3.0 19.1 - - - +
1026A PHE* 3.5 11.0 - - - +
1027A VAL 2.6 4.6 + - - -
1028A VAL* 1.3 74.4 - - - +
1030A ARG* 1.3 61.7 + - + +
1031A ARG 2.8 9.7 + - - -
1033A PHE* 3.1 25.3 + - + +
1034A SER 3.2 5.5 + - - -
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Residues in contact with ARG1030 (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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538A THR* 3.1 45.1 + - + +
542A LEU* 3.8 34.1 - - - +
903A LEU* 4.7 3.6 - - - +
1023A PRO* 4.1 12.5 - - - +
1026A PHE* 2.8 73.5 + - - +
1027A VAL* 3.6 4.7 - - - +
1029A VAL* 1.3 77.3 - - + +
1031A ARG* 1.3 91.9 + - + +
1034A SER* 2.9 28.5 + - - +
1035A ARG* 3.9 1.7 + - - -
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Residues in contact with ARG1031 (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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542A LEU* 5.3 5.5 - - - +
896A SER* 4.1 26.5 - - - +
899A PHE* 4.4 28.1 + - + +
900A SER 4.7 2.2 - - - +
903A LEU* 4.7 21.7 - - - +
1027A VAL* 2.8 41.7 + - + +
1028A VAL* 4.5 1.3 - - - +
1029A VAL 2.8 3.0 + - - -
1030A ARG* 1.3 106.5 + - - +
1032A ARG* 1.3 60.3 + - - +
1033A PHE 3.0 4.5 + - - -
1034A SER* 3.5 6.9 + - - -
1035A ARG* 4.1 22.2 + - - +
1036A LYS 3.2 10.7 - - - +
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Residues in contact with ARG1032 (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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894A SER* 5.2 5.9 - - - -
896A SER* 3.3 30.4 - - - +
897A ILE* 6.0 0.4 - - + -
950A LYS* 3.4 28.2 - - + +
953A MET* 3.1 39.8 + - - +
954A ASP* 4.2 17.2 + - - -
1028A VAL* 2.9 34.3 + - + +
1031A ARG* 1.3 75.9 - - - +
1033A PHE* 1.3 71.4 + - + +
1036A LYS 3.0 12.5 - - - +
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Residues in contact with PHE1033 (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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953A MET* 3.4 37.5 - - + -
958A LYS* 3.2 35.9 - - - -
960A LEU* 3.1 52.3 - - + -
1028A VAL 4.0 6.5 - - - -
1029A VAL* 3.1 14.1 + - + +
1031A ARG 3.0 1.0 - - - -
1032A ARG* 1.3 94.1 - - + +
1034A SER* 1.3 70.7 + - - +
1035A ARG 2.5 4.4 + - - -
1036A LYS 2.5 22.5 + - - +
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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