Contacts of the helix formed by residues 801 - 805 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754I THR 3.4 25.6 - - - +
755I ARG 3.5 9.6 - - - +
757I VAL* 4.5 2.0 - - - -
760I LEU* 3.2 12.7 - - - +
762I GLN* 2.7 20.9 + - - +
794I ASN* 3.9 17.7 - - - +
800I GLY* 1.3 76.8 - - - +
802I LEU* 1.3 66.7 + - - +
803I SER* 3.2 25.4 - - - +
804I SER* 3.0 19.8 + - - -
805I ASN* 3.9 3.3 + - - -
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Residues in contact with LEU 802 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752I LEU 3.1 27.4 - - - +
753I THR* 3.8 21.7 + - + -
757I VAL* 4.3 9.6 - - + -
760I LEU* 4.3 9.2 - - + -
801I CYS* 1.3 68.1 - - + +
803I SER* 1.3 53.9 + - - +
804I SER 2.8 6.9 + - - -
805I ASN* 2.7 26.3 + - + +
806I ILE* 2.9 31.2 + - + +
811I LEU* 4.7 0.4 - - - -
919I TRP* 3.4 37.2 - - + -
928I VAL* 4.6 6.3 - - + -
1003I TYR* 4.5 6.7 - - - +
1008I LEU* 4.2 24.5 - - + +
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Residues in contact with SER 803 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753I THR 3.0 19.7 + - - -
754I THR* 4.6 7.3 + - - -
786I TYR* 3.5 17.8 - - - +
787I ILE* 3.5 42.2 + - - +
788I SER* 4.5 7.4 - - - -
789I SER 5.3 1.4 + - - -
801I CYS* 3.2 22.9 - - - +
802I LEU* 1.3 74.8 - - - +
804I SER* 1.3 57.8 + - - +
806I ILE 3.7 5.3 - - - +
811I LEU* 3.7 12.8 - - - -
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Residues in contact with SER 804 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762I GLN* 3.2 39.7 + - - -
764I HIS 3.1 26.5 - - - +
765I ASN* 3.8 3.1 - - - -
766I GLY* 3.7 22.9 + - - +
786I TYR* 3.6 3.2 - - - -
787I ILE 5.3 0.7 + - - -
801I CYS* 3.0 12.6 + - - -
802I LEU 2.9 1.4 - - - -
803I SER* 1.3 81.6 + - - +
805I ASN* 1.3 63.5 + - - +
806I ILE 3.7 0.2 - - - -
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Residues in contact with ASN 805 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760I LEU* 4.0 6.8 - - - +
761I GLN 3.0 17.9 + - - +
762I GLN* 3.4 10.1 - - - +
763I ILE* 3.3 23.7 - - - +
764I HIS* 5.0 4.9 - - - +
786I TYR* 3.8 9.0 + - - -
801I CYS 4.4 5.2 - - - -
802I LEU* 2.7 11.3 + - - +
804I SER* 1.3 83.6 + - - +
806I ILE* 1.3 62.4 + - - +
807I PRO* 3.9 2.6 - - - +
919I TRP* 3.4 61.6 + - + +
925I ARG* 3.6 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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