Contacts of the helix formed by residues 983 - 995 (chain B) in PDB entry 1SO2
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 GLN 983 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960B TYR* 5.0 0.6 + - - -
976B PHE* 3.6 34.6 + - + +
981B SER* 4.0 13.6 + - - +
982B PRO* 1.3 86.0 + - - +
984B LEU* 1.3 64.6 + - - +
985B ALA 3.3 2.5 - - - -
986B LYS* 3.2 19.9 + - + +
987B LEU* 2.9 22.2 + - - +
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Residues in contact with LEU 984 (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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451B HG9 3.7 35.4 - - + -
452B HG9 5.9 4.3 - - + -
952B THR* 3.8 21.3 - - + -
956B VAL* 3.6 30.3 - - + -
960B TYR* 5.3 8.0 + - - +
982B PRO* 3.7 4.5 - - + +
983B GLN* 1.3 75.0 - - - +
985B ALA* 1.3 63.9 + - - +
987B LEU* 3.4 9.3 + - + +
988B GLN* 3.1 25.7 + - + +
1072B TRP* 4.0 14.8 - - + -
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Residues in contact with ALA 985 (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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452B HG9 3.5 38.4 - - + +
983B GLN 3.3 0.6 - - - -
984B LEU* 1.3 78.0 - - - +
986B LYS* 1.3 59.8 + - - +
988B GLN 3.2 1.9 + - - -
989B GLU* 2.8 33.3 + - - +
1072B TRP* 3.6 32.5 - - + +
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Residues in contact with LYS 986 (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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976B PHE* 3.9 21.3 - - + -
983B GLN* 3.2 26.6 + - + +
985B ALA* 1.3 76.5 - - - +
987B LEU* 1.3 58.6 + - - +
989B GLU* 4.3 8.8 + - - +
990B SER* 2.9 38.3 + - - -
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Residues in contact with LEU 987 (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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462B 666 3.6 50.5 - - + -
955B ILE* 5.1 2.2 - - + -
956B VAL* 4.6 15.9 - - + -
959B PHE* 4.1 24.2 - - + -
976B PHE* 3.5 28.0 - - + +
983B GLN 2.9 13.0 + - - +
984B LEU* 3.4 11.4 - - - +
986B LYS* 1.3 77.2 - - - +
988B GLN* 1.3 82.3 + - - +
990B SER* 3.6 0.7 - - - -
991B PHE* 2.9 23.2 + - + +
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Residues in contact with GLN 988 (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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462B 666 2.9 39.4 + - - -
948B HIS* 3.6 10.0 - - - -
952B THR* 3.3 32.1 - - + +
955B ILE* 4.2 8.5 - - - +
984B LEU* 3.1 15.8 + - + +
987B LEU* 1.3 94.0 - - - +
989B GLU* 1.3 64.7 + - - +
991B PHE* 4.6 3.2 - - - -
992B ILE* 2.9 38.4 + - + +
1072B TRP* 3.7 35.2 - - + -
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Residues in contact with GLU 989 (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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985B ALA 2.8 22.1 + - - +
986B LYS* 4.0 8.4 + - - +
988B GLN* 1.3 72.9 - - - +
990B SER* 1.3 67.4 + - - +
992B ILE* 4.8 1.3 - - - -
993B THR* 2.6 58.8 + - - +
994B HIS* 5.7 0.7 + - - -
1069B HIS* 3.6 18.2 + - - +
1072B TRP* 3.9 17.8 - - + +
1073B LYS* 3.9 32.8 - - + +
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Residues in contact with SER 990 (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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462B 666 3.5 16.5 - - - +
976B PHE* 5.1 4.4 - - - -
986B LYS* 2.9 25.1 + - - -
987B LEU* 3.6 3.6 - - - -
989B GLU* 1.3 84.2 + - - +
991B PHE* 1.3 57.9 + - - +
993B THR* 3.0 2.6 + - - -
994B HIS* 2.7 60.7 + - - +
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Residues in contact with PHE 991 (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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462B 666 3.5 95.7 - + + +
895B LEU* 4.0 10.3 - - + -
938B ILE* 3.9 17.5 - - + -
941B PRO* 5.3 1.6 - - + -
987B LEU* 2.9 22.2 + - + +
988B GLN* 4.0 5.2 - - - +
990B SER* 1.3 73.8 - - - +
992B ILE* 1.3 57.2 + - + +
995B ILE* 3.0 62.0 + - + +
996B VAL* 3.0 32.0 + - + -
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Residues in contact with ILE 992 (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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941B PRO* 3.8 33.4 - - + -
948B HIS* 4.8 1.8 - - + -
988B GLN* 2.9 26.0 + - - +
989B GLU* 4.0 1.3 - - - +
991B PHE* 1.3 77.5 - - + +
993B THR* 1.3 61.5 + - - +
996B VAL* 4.1 6.7 - - + -
997B GLY* 2.7 30.7 + - - +
1065B LEU* 4.0 24.0 - - + +
1068B ASN* 4.3 2.7 - - + +
1069B HIS* 3.4 47.8 - - + +
1072B TRP* 4.2 16.8 - - + +
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Residues in contact with THR 993 (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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989B GLU* 2.6 40.5 + - - +
990B SER* 3.0 5.7 + - - -
992B ILE* 1.3 79.1 - - - +
994B HIS* 1.3 77.8 + - + +
998B PRO* 3.2 17.5 - - - +
1069B HIS* 2.9 16.4 - - + -
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Residues in contact with HIS 994 (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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462B 666 5.3 1.6 - - + -
898B HIS* 4.4 0.5 + - - -
899B PHE* 3.7 26.8 - - + -
989B GLU* 5.7 0.6 + - - -
990B SER* 2.7 45.5 + - - -
993B THR* 1.3 91.4 + - + +
995B ILE* 1.3 69.2 + - + +
998B PRO* 3.2 17.9 - - - +
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Residues in contact with ILE 995 (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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462B 666 3.9 15.0 - - + -
895B LEU* 4.1 11.7 - - + -
898B HIS* 3.4 37.2 + - + +
899B PHE* 5.2 4.9 - - + -
938B ILE* 3.9 14.6 - - + -
991B PHE* 3.0 52.6 + - + +
993B THR 3.7 0.6 - - - -
994B HIS* 1.3 95.9 - - + +
996B VAL* 1.3 68.9 + - - +
997B GLY 3.4 0.7 - - - -
998B PRO* 3.6 1.8 - - - +
999B LEU* 3.3 21.3 + - - +
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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