Contacts of the helix formed by residues 939 - 943 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A TRP* 4.2 20.2 - - + -
744A ASP* 3.6 22.3 + - - +
745A VAL* 4.9 1.2 - - - +
748A ALA* 4.2 8.6 - - + +
935A LEU* 3.1 18.9 + - + +
936A ALA* 2.7 22.9 - - - +
937A ASP 3.5 1.4 - - - +
938A ILE* 1.3 75.9 - - - +
940A GLY* 1.3 72.1 + - - +
941A PRO 3.5 0.4 - - - -
942A ALA* 2.7 24.7 + - - +
943A LYS* 3.1 41.4 + - - +
951A TRP* 5.3 0.6 - - - +
996A VAL* 5.8 0.4 - - - -
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Residues in contact with GLY 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A ASP 5.3 0.2 + - - -
938A ILE 3.1 4.9 + - - -
939A ASN* 1.3 85.6 - - - +
941A PRO* 1.3 61.0 - - - +
942A ALA 2.9 3.8 + - - -
943A LYS* 3.2 18.2 + - - +
948A HIS* 3.5 17.6 + - - +
951A TRP* 4.7 17.7 - - - -
2111A IBM 3.8 13.8 - - - -
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Residues in contact with PRO 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A ILE 3.7 7.9 - - - +
940A GLY* 1.3 83.8 - - - +
942A ALA* 1.3 56.5 + - - +
943A LYS 3.4 1.6 - - - -
948A HIS* 3.3 31.4 - - + +
991A PHE* 4.6 2.9 - - + -
992A ILE* 3.9 22.0 - - + -
996A VAL* 3.8 26.2 - - + -
1065A LEU* 3.2 30.3 - - + -
1068A ASN* 2.9 18.6 + - + +
2111A IBM 3.9 14.1 - - - +
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Residues in contact with ALA 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A TRP* 3.0 22.5 + - + -
935A LEU* 5.6 1.8 - - + -
939A ASN* 2.7 22.8 + - - +
941A PRO* 1.3 73.6 - - - +
943A LYS* 1.3 60.6 + - - +
996A VAL* 5.3 2.5 - - + -
1000A CYS* 5.0 5.6 - - - -
1061A LEU* 3.6 39.2 - - + +
1064A HIS* 3.2 15.6 - - - +
1065A LEU* 4.1 10.3 - - + +
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Residues in contact with LYS 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677A TRP* 3.3 56.3 + - + +
678A ASN* 3.5 7.6 - - - +
679A PHE* 5.0 3.8 + - - +
681A ILE* 6.2 0.6 - - - +
744A ASP* 3.3 25.6 + - - -
747A HIS* 4.9 5.9 + - - -
748A ALA* 5.7 1.6 - - - -
939A ASN* 3.1 29.9 - - - +
940A GLY* 3.2 12.4 + - - +
942A ALA* 1.3 79.6 - - - +
944A VAL* 1.3 71.5 + - - +
947A LEU* 4.0 30.5 - - + +
951A TRP* 5.0 4.4 - - + +
1064A HIS* 3.4 10.5 + - - +
1068A ASN* 3.0 19.1 + - - -
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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