Contacts of the helix formed by residues 801 - 805 (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 CYS 801 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753G THR 4.9 0.2 - - - -
754G THR 3.4 26.5 - - - +
755G ARG 3.5 9.2 - - - +
757G VAL* 4.5 1.6 - - - -
760G LEU* 3.1 16.4 - - - +
762G GLN* 3.1 22.4 + - - +
794G ASN* 3.9 11.4 - - - +
800G GLY* 1.3 76.6 - - - +
802G LEU* 1.3 66.9 + - - +
803G SER* 3.1 26.2 - - - +
804G SER* 3.0 20.5 + - - -
805G ASN* 3.9 3.5 + - - -
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Residues in contact with LEU 802 (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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752G LEU 3.1 27.8 - - - +
753G THR* 3.8 20.8 + - + -
757G VAL* 4.3 10.1 - - + -
760G LEU* 4.3 9.6 - - + -
801G CYS* 1.3 67.3 - - + +
803G SER* 1.3 53.9 + - - +
804G SER 2.7 7.2 + - - -
805G ASN* 2.7 26.0 + - + +
806G ILE* 2.9 30.1 + - + +
811G LEU* 4.7 0.9 - - - -
919G TRP* 3.4 37.7 - - + -
928G VAL* 4.6 6.5 - - + -
1003G TYR* 4.5 7.4 - - - +
1008G LEU* 4.2 24.2 - - + +
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Residues in contact with SER 803 (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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753G THR 3.0 18.6 + - - -
754G THR* 4.6 6.5 + - - -
786G TYR* 3.5 18.0 - - - +
787G ILE* 3.5 42.4 + - - +
788G SER* 4.5 7.4 - - - -
789G SER 5.2 1.5 + - - -
801G CYS* 3.1 22.5 - - - -
802G LEU* 1.3 74.6 - - - +
804G SER* 1.3 56.9 + - - +
806G ILE 3.7 4.6 - - - +
811G LEU* 3.7 12.6 - - - -
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Residues in contact with SER 804 (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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762G GLN* 2.7 34.2 + - - -
764G HIS 3.1 6.6 - - - +
765G ASN* 3.1 37.3 + - - +
766G GLY 4.5 3.1 - - - +
786G TYR* 3.6 9.2 - - - -
787G ILE 5.4 0.9 + - - -
801G CYS* 3.0 10.3 + - - -
802G LEU 2.7 1.4 + - - -
803G SER* 1.3 81.5 + - - +
805G ASN* 1.3 65.8 + - - +
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Residues in contact with ASN 805 (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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760G LEU* 4.0 9.5 - - - +
761G GLN 3.1 18.0 - - - +
762G GLN* 3.6 25.0 - - - +
764G HIS* 3.9 10.3 - - - +
765G ASN 3.8 5.3 - - - +
786G TYR* 3.8 8.2 + - - -
801G CYS 4.4 5.4 - - - -
802G LEU* 2.7 11.1 + - - +
804G SER* 1.3 83.8 + - - +
806G ILE* 1.3 62.3 + - - +
807G PRO* 3.9 2.4 - - - +
919G TRP* 3.3 56.4 + - + +
925G ARG* 3.6 15.1 - - - -
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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