Contacts of the helix formed by residues 983 - 995 (chain L) in PDB entry 1SOJ
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960L TYR* 4.5 1.2 + - - -
976L PHE* 4.0 29.8 + - + +
981L SER* 3.7 13.4 + - - +
982L PRO* 1.3 80.4 - - - +
984L LEU* 1.3 66.1 + - - +
985L ALA 3.3 2.5 - - - -
986L LYS* 2.8 46.4 + - + +
987L LEU* 2.9 10.2 + - - +
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Residues in contact with LEU 984 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952L THR* 3.6 20.9 - - + -
956L VAL* 3.3 36.8 - - + -
960L TYR* 4.9 7.3 + - - +
982L PRO* 3.7 5.3 - - + +
983L GLN* 1.3 74.2 - - - +
985L ALA* 1.3 64.0 + - - +
987L LEU* 3.1 9.5 + - + +
988L GLN* 3.0 29.1 + - + +
1072L TRP* 3.7 24.9 - - + -
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Residues in contact with ALA 985 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983L GLN 3.1 0.8 + - - -
984L LEU* 1.3 78.9 - - - +
986L LYS* 1.3 62.2 + - - +
989L GLU* 3.0 26.5 + - - +
1072L TRP* 3.4 39.8 - - + +
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Residues in contact with LYS 986 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976L PHE* 3.8 20.9 - - + -
983L GLN* 2.8 44.4 + - + +
985L ALA* 1.3 72.3 - - - +
987L LEU* 1.3 65.6 + - - +
989L GLU* 3.5 6.3 - - - +
990L SER* 3.0 26.5 + - - -
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Residues in contact with LEU 987 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955L ILE* 5.7 0.9 - - + -
956L VAL* 4.2 23.1 - - + -
959L PHE* 4.1 26.2 - - + -
976L PHE* 3.3 47.4 - - + +
983L GLN 2.9 6.6 + - - +
984L LEU* 3.2 13.2 - - + +
986L LYS* 1.3 78.6 - - - +
988L GLN* 1.3 78.9 + - - +
990L SER* 3.5 3.1 - - - -
991L PHE* 2.9 22.7 + - + +
2122L IBM 3.9 18.4 - - + +
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Residues in contact with GLN 988 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948L HIS* 3.5 9.1 - - - -
952L THR* 2.9 42.4 + - + +
955L ILE* 5.1 0.4 - - - +
984L LEU* 3.0 17.0 + - + +
987L LEU* 1.3 82.1 - - - +
989L GLU* 1.3 63.5 + - - +
991L PHE* 4.3 3.1 - - - -
992L ILE* 2.9 35.7 + - + +
1072L TRP* 3.5 43.5 - - + +
2122L IBM 2.9 41.3 + - - -
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Residues in contact with GLU 989 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985L ALA 3.0 22.7 + - - +
986L LYS* 3.5 6.8 - - - +
988L GLN* 1.3 78.5 - - - +
990L SER* 1.3 69.8 + - - +
992L ILE* 3.5 3.5 + - - +
993L THR* 3.0 49.8 + - - +
994L HIS* 5.7 0.5 + - - -
1069L HIS* 3.0 22.8 + - + -
1072L TRP* 4.0 21.7 - - + +
1073L LYS* 4.2 16.0 - - + +
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Residues in contact with SER 990 (chain L).
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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976L PHE* 5.6 6.1 - - - -
986L LYS* 3.0 20.1 + - - -
987L LEU* 3.5 4.5 - - - -
989L GLU* 1.3 83.2 + - - +
991L PHE* 1.3 57.4 + - - +
993L THR* 2.9 1.9 + - - -
994L HIS* 2.8 58.1 + - - +
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Residues in contact with PHE 991 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895L LEU* 5.0 3.4 - - + -
938L ILE* 4.0 10.1 - - + -
941L PRO* 4.3 7.6 - - + -
987L LEU* 2.9 16.4 + - + +
988L GLN* 3.7 5.2 - - - +
990L SER* 1.3 75.9 - - - +
992L ILE* 1.3 61.1 + - + +
995L ILE* 3.0 66.7 + - + +
996L VAL* 3.1 39.6 + - + -
2122L IBM 3.3 83.0 - + + +
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Residues in contact with ILE 992 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941L PRO* 3.5 32.3 - - + -
948L HIS* 4.1 6.7 - - + +
988L GLN* 2.9 23.7 + - + +
989L GLU* 4.0 4.3 - - - +
991L PHE* 1.3 77.1 - - + +
993L THR* 1.3 57.7 + - - +
996L VAL* 4.5 3.6 - - - -
997L GLY* 3.2 25.7 + - - +
1065L LEU* 4.1 29.6 - - + +
1068L ASN* 4.5 1.1 - - + -
1069L HIS* 3.6 37.2 - - + +
1072L TRP* 3.8 26.9 - - + +
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Residues in contact with THR 993 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989L GLU* 3.0 22.9 + - - +
990L SER* 2.9 7.2 + - - -
992L ILE* 1.3 80.9 - - - +
994L HIS* 1.3 83.6 + - + +
995L ILE 3.6 0.4 - - - -
997L GLY* 4.7 0.4 - - - -
998L PRO* 3.2 15.8 - - - +
1069L HIS* 2.8 28.2 + - - -
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Residues in contact with HIS 994 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898L HIS* 4.3 0.2 + - - -
899L PHE* 3.4 29.4 - - + -
989L GLU* 5.7 0.6 + - - -
990L SER* 2.8 46.0 + - - +
993L THR* 1.3 93.7 + - + +
995L ILE* 1.3 65.5 + - + +
998L PRO* 3.3 15.1 - - - +
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Residues in contact with ILE 995 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895L LEU* 4.6 16.2 - - + -
898L HIS* 3.6 28.4 + - + +
899L PHE* 4.8 6.5 - - + -
938L ILE* 3.7 22.2 - - + -
991L PHE* 3.0 44.5 + - + +
993L THR 3.6 0.8 - - - -
994L HIS* 1.3 89.3 - - + +
996L VAL* 1.3 69.2 + - - +
997L GLY 3.2 0.4 - - - -
998L PRO* 3.2 13.9 - - - +
999L LEU* 3.2 13.2 + - - +
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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