Contacts of the helix formed by residues 939 - 943 (chain C) 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 ASN 939 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677C TRP* 4.2 20.4 - - + -
741C HIS* 6.1 0.2 - - - -
744C ASP* 3.5 21.6 + - - +
745C VAL* 4.9 1.4 - - - +
748C ALA* 4.2 7.5 - - - +
935C LEU* 3.1 18.2 + - + +
936C ALA* 2.8 23.1 - - - +
937C ASP 3.5 1.8 + - - +
938C ILE* 1.3 76.1 - - - +
940C GLY* 1.3 70.6 + - - +
941C PRO 3.5 0.7 - - - -
942C ALA* 2.7 24.4 + - - -
943C LYS* 3.1 41.8 + - - +
951C TRP* 5.2 0.4 - - - +
996C VAL* 5.8 0.7 - - - -
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Residues in contact with GLY 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937C ASP 5.4 0.2 + - - -
938C ILE* 3.1 5.9 + - - +
939C ASN* 1.3 86.7 - - - +
941C PRO* 1.3 61.4 - - - +
942C ALA 2.9 3.5 + - - -
943C LYS* 3.2 18.0 + - - +
948C HIS* 3.5 18.1 + - - +
951C TRP* 4.7 16.6 - - - -
2113C IBM 3.7 13.7 - - - -
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Residues in contact with PRO 941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C ILE 3.7 4.5 - - - +
940C GLY* 1.3 84.0 - - - +
942C ALA* 1.3 55.6 + - - +
943C LYS 3.4 2.7 - - - -
948C HIS* 3.3 30.7 - - + +
991C PHE* 4.6 2.7 - - + -
992C ILE* 3.9 21.5 - - + -
996C VAL* 3.8 25.6 - - + -
1065C LEU* 3.2 30.7 - - + +
1068C ASN* 2.9 19.0 + - + +
2113C IBM 3.7 19.1 - - - +
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Residues in contact with ALA 942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677C TRP* 3.0 22.7 + - + -
935C LEU* 5.6 2.0 - - + -
939C ASN* 2.7 23.1 + - - +
941C PRO* 1.3 73.9 - - - +
943C LYS* 1.3 61.0 + - - +
996C VAL* 5.3 2.7 - - + -
1000C CYS* 5.0 5.4 - - - -
1061C LEU* 3.6 39.6 - - + +
1064C HIS* 3.2 15.1 - - - +
1065C LEU* 4.1 9.6 - - + +
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Residues in contact with LYS 943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677C TRP* 3.2 56.2 + - + +
678C ASN* 3.5 7.2 - - - +
679C PHE* 5.0 4.2 + - - +
681C ILE* 6.2 0.8 - - - +
744C ASP* 3.3 26.4 + - - -
747C HIS* 5.0 5.9 + - - -
748C ALA* 5.7 1.1 - - - -
939C ASN* 3.1 29.9 - - - +
940C GLY* 3.2 12.9 + - - +
942C ALA* 1.3 78.3 - - - +
944C VAL* 1.3 71.8 + - - +
947C LEU* 4.0 29.2 - - + +
948C HIS* 4.5 0.4 - - - +
951C TRP* 5.0 4.0 - - + +
1064C HIS* 3.3 11.8 + - - +
1068C ASN* 3.0 19.4 + - - -
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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