Contacts of the helix formed by residues 986 - 994 (chain A) in PDB entry 1M8X
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 LEU 986 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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954A VAL* 4.3 7.4 - - + -
977A CYS* 3.8 30.1 - - + +
978A ILE* 3.5 36.6 - - + +
981A VAL* 3.7 28.0 - - + +
982A GLN 3.8 8.5 - - - +
983A PRO* 2.8 18.3 + - + +
985A SER* 1.3 78.1 - - - +
987A GLN* 1.3 64.0 + - - +
988A PHE* 3.1 7.9 - - - -
989A ILE* 2.9 32.3 + - + +
990A ILE* 3.3 10.7 + - + +
1016A HIS* 6.0 0.7 - - + -
1017A CYS* 4.5 12.8 - - - -
1021A GLN* 4.3 1.3 - - - -
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Residues in contact with GLN 987 (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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983A PRO 3.6 2.0 + - - -
984A GLN* 3.6 14.9 + - - +
985A SER 3.3 1.8 - - - -
986A LEU* 1.3 78.1 - - - +
988A PHE* 1.3 57.3 + - - +
990A ILE* 3.0 20.1 + - - +
991A ASP* 2.8 60.2 + - - +
994A LYS* 4.9 6.5 - - - +
1020A ASP* 5.7 2.1 + - - +
1021A GLN* 2.9 35.6 + - - +
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Residues in contact with PHE 988 (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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954A VAL* 3.2 35.0 - - + -
955A ARG* 5.2 2.5 - - + -
957A LEU* 3.8 11.9 - - + -
958A ASP* 3.6 51.6 - - + +
959A GLY 4.8 0.7 - - - -
961A VAL* 3.7 19.8 - - + +
985A SER 3.2 26.2 - - - -
986A LEU* 3.8 3.4 - - - -
987A GLN* 1.3 79.3 - - - +
989A ILE* 1.3 82.1 + - + +
991A ASP* 3.6 13.4 + - - +
992A ALA* 3.3 20.8 + - - +
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Residues in contact with ILE 989 (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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957A LEU* 6.0 2.5 - - + -
961A VAL* 3.9 17.5 - - + -
974A VAL* 4.0 26.7 - - + -
977A CYS* 4.9 7.6 - - + -
978A ILE* 4.6 7.9 - - + -
986A LEU* 2.9 30.9 + - + +
988A PHE* 1.3 105.9 - - + +
990A ILE* 1.3 67.3 + - + +
992A ALA* 3.2 1.9 + - - +
993A PHE* 3.1 52.7 + - + -
1013A ILE* 4.3 14.6 - - + -
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Residues in contact with ILE 990 (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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986A LEU 3.7 11.2 - - - +
987A GLN* 3.0 23.7 + - - +
989A ILE* 1.3 75.9 - - + +
991A ASP* 1.3 67.9 + - - +
993A PHE* 2.8 17.7 + - - +
994A LYS* 3.2 27.1 + - + +
1013A ILE* 3.7 39.3 - - + -
1017A CYS* 4.1 9.2 - - - -
1021A GLN* 3.8 50.0 - - + +
1024A PRO* 4.9 0.9 - - + -
1025A ILE* 4.6 7.1 - - + +
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Residues in contact with ASP 991 (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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987A GLN* 2.8 52.9 + - - +
988A PHE* 3.6 13.8 + - - +
989A ILE 3.4 0.2 - - - -
990A ILE* 1.3 70.8 - - - +
992A ALA* 1.3 61.7 + - - +
993A PHE 3.5 0.2 + - - -
994A LYS* 3.5 31.3 + - + +
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Residues in contact with ALA 992 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961A VAL* 3.8 26.5 - - + -
962A LEU* 4.1 23.1 - - + +
988A PHE 3.3 15.5 + - - +
989A ILE 3.2 6.9 + - - +
990A ILE 3.0 1.2 - - - -
991A ASP* 1.3 80.9 - - - +
993A PHE* 1.3 59.2 + - + +
994A LYS 3.4 4.0 - - - +
996A GLN* 4.7 5.4 - - - +
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Residues in contact with PHE 993 (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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961A VAL* 4.1 5.2 - - + -
962A LEU* 4.6 2.5 - - + -
965A VAL* 3.8 24.9 - - + -
989A ILE* 3.1 39.5 + - + +
990A ILE* 2.8 9.8 + - - +
992A ALA* 1.3 77.2 - - - +
994A LYS* 1.3 60.0 + - - +
995A GLY 3.1 0.7 + - - -
996A GLN* 2.8 22.9 + - - -
997A VAL* 3.3 13.4 + - + +
1000A LEU* 3.2 32.8 - - + -
1006A GLY 4.7 0.9 - - - -
1009A VAL* 3.5 26.2 - - + -
1010A ILE* 3.3 37.0 - - + -
1013A ILE* 3.9 15.0 - - + -
1025A ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 994 (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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987A GLN* 4.9 4.4 - - - +
990A ILE* 3.2 25.9 + - + +
991A ASP* 3.6 25.9 + - - +
992A ALA 3.4 5.2 - - - +
993A PHE* 1.3 76.0 - - - +
995A GLY* 1.3 58.1 + - - +
996A GLN* 3.4 4.9 + - - +
997A VAL* 5.1 1.1 - - - -
1020A ASP 5.5 3.0 + - - -
1024A PRO* 3.9 34.0 - - + +
1025A ILE* 5.7 2.7 - - + -
1028A GLU* 3.8 6.7 - - - +
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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