Contacts of the helix formed by residues 983 - 995 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960G TYR* 4.8 0.6 + - - -
976G PHE* 3.6 30.7 + - + +
981G SER 4.0 8.3 - - - +
982G PRO* 1.3 81.4 - - - +
984G LEU* 1.3 55.9 + - - +
985G ALA 3.3 2.5 - - - -
986G LYS* 3.0 39.5 + - + +
987G LEU* 2.7 35.1 + - - +
881L ARG* 4.8 11.1 + - - -
922L GLU* 3.5 14.0 - - - +
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Residues in contact with LEU 984 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952G THR* 3.7 22.9 - - + -
956G VAL* 3.6 33.7 - - + -
960G TYR* 4.7 9.6 + - - +
982G PRO* 3.7 3.0 - - + +
983G GLN* 1.3 74.5 - - - +
985G ALA* 1.3 59.2 + - - +
987G LEU* 3.1 9.4 + - + +
988G GLN* 2.9 35.2 + - + +
1072G TRP* 4.1 18.8 - - + -
920L SER* 3.4 33.7 - - - +
922L GLU* 2.8 14.4 + - - +
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Residues in contact with ALA 985 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984G LEU* 1.3 72.4 - - - +
986G LYS* 1.3 59.4 + - - +
988G GLN* 3.3 0.7 + - - +
989G GLU* 2.8 34.5 + - - +
1072G TRP* 3.6 23.9 - - + +
921L ASN* 3.4 26.0 - - - +
922L GLU* 2.9 21.2 + - - +
923L ASN* 3.8 19.1 - - - +
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Residues in contact with LYS 986 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976G PHE* 3.8 17.3 - - + -
983G GLN* 3.0 45.9 + - + +
985G ALA* 1.3 78.5 - - - +
987G LEU* 1.3 57.4 + - - +
989G GLU* 3.8 5.6 - - - +
990G SER* 2.9 34.5 + - - -
922L GLU* 3.6 3.0 + - - +
923L ASN* 5.3 1.4 + - - +
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Residues in contact with LEU 987 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955G ILE* 5.4 0.7 - - + -
956G VAL* 3.9 26.9 - - + -
959G PHE* 4.1 18.8 - - + -
976G PHE* 3.4 46.1 - - + +
983G GLN 2.7 16.3 + - - +
984G LEU* 3.2 10.8 - - + +
986G LYS* 1.3 73.9 - - - +
988G GLN* 1.3 68.8 + - - +
990G SER* 3.5 3.2 - - - -
991G PHE* 2.8 30.2 + - + +
2117G IBM 3.9 25.4 - - + +
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Residues in contact with GLN 988 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948G HIS* 3.6 9.9 - - - -
952G THR* 2.8 46.9 + - + +
984G LEU* 2.9 18.5 + - + +
987G LEU* 1.3 77.6 - - - +
989G GLU* 1.3 67.0 + - - +
991G PHE* 3.7 3.7 - - - +
992G ILE* 3.0 32.2 + - + +
1072G TRP* 3.5 39.3 - - + +
2117G IBM 2.8 42.6 + - - +
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Residues in contact with GLU 989 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985G ALA 2.8 23.0 + - - +
986G LYS* 3.8 6.6 - - - +
988G GLN* 1.3 73.3 - - - +
990G SER* 1.3 71.6 + - - +
993G THR* 2.7 45.3 + - - +
994G HIS* 5.9 0.2 + - - -
1069G HIS* 3.0 17.8 + - + +
1072G TRP* 3.9 22.6 - - - +
1073G LYS* 3.4 29.7 - - + -
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Residues in contact with SER 990 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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976G PHE* 5.1 9.6 - - - -
986G LYS* 2.9 22.2 + - - -
987G LEU* 3.5 5.4 - - - -
989G GLU* 1.3 85.7 + - - +
991G PHE* 1.3 62.5 + - - +
993G THR* 3.4 0.4 + - - -
994G HIS* 3.0 46.2 + - - +
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Residues in contact with PHE 991 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895G LEU* 4.8 2.5 - - + -
938G ILE* 4.0 11.0 - - + -
941G PRO* 4.6 6.7 - - + -
987G LEU* 2.8 20.8 + - + +
988G GLN* 3.7 7.2 - - - +
989G GLU 3.3 0.2 - - - -
990G SER* 1.3 74.1 - - - +
992G ILE* 1.3 60.3 + - + +
994G HIS* 5.5 0.2 - - - -
995G ILE* 2.8 66.3 + - + +
996G VAL* 3.2 37.0 + - + -
2117G IBM 3.3 82.6 - + + +
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Residues in contact with ILE 992 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941G PRO* 3.8 32.3 - - + -
948G HIS* 4.8 0.4 - - + +
988G GLN* 3.0 19.0 + - + +
989G GLU 3.8 2.7 - - - +
991G PHE* 1.3 77.6 - - + +
993G THR* 1.3 61.5 + - - +
996G VAL* 4.4 4.0 - - - -
997G GLY* 2.7 36.9 + - - +
1065G LEU* 4.0 23.1 - - + -
1068G ASN* 4.4 1.6 - - + -
1069G HIS* 3.7 44.9 - - + +
1072G TRP* 3.8 25.1 - - + +
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Residues in contact with THR 993 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989G GLU* 2.7 40.1 + - - +
990G SER* 3.8 3.4 - - - -
992G ILE* 1.3 77.0 - - - +
994G HIS* 1.3 83.7 + - + +
997G GLY* 4.7 0.4 - - - -
998G PRO* 3.1 18.4 - - - +
1069G HIS* 3.0 20.2 + - - -
1073G LYS* 4.9 0.2 - - - -
899K PHE* 4.6 19.1 - - + -
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Residues in contact with HIS 994 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899G PHE* 3.4 27.8 - - + -
989G GLU* 5.9 0.2 + - - -
990G SER* 3.0 40.4 + - - +
993G THR* 1.3 90.8 + - + +
995G ILE* 1.3 67.8 + - + +
998G PRO* 3.1 17.9 - - - +
899K PHE* 3.7 44.4 - + - -
994K HIS* 5.1 9.9 + - + +
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Residues in contact with ILE 995 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895G LEU* 4.2 18.6 - - + -
898G HIS* 3.2 46.4 + - + +
899G PHE* 4.7 7.2 - - + -
938G ILE* 3.7 15.0 - - + -
991G PHE* 2.8 50.6 + - + +
993G THR 3.7 0.4 - - - -
994G HIS* 1.3 85.2 - - + +
996G VAL* 1.3 67.1 + - - +
997G GLY 3.3 0.9 - - - -
998G PRO* 3.4 2.3 - - - +
999G LEU* 3.3 14.6 + - - +
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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