Contacts of the helix formed by residues 939 - 943 (chain B) in PDB entry 1SO2
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B TRP* 4.6 12.6 - - + -
744B ASP* 2.7 33.5 + - - +
748B ALA* 3.9 8.8 - - - +
935B LEU* 3.1 14.0 + - + +
936B ALA* 3.3 19.6 - - - +
937B ASP 3.5 2.2 + - - -
938B ILE* 1.3 77.0 - - - +
940B GLY* 1.3 76.5 + - - +
941B PRO* 3.4 0.7 - - - -
942B ALA* 2.8 23.7 + - - +
943B LYS* 3.3 35.2 + - - +
951B TRP* 4.9 2.8 - - - -
996B VAL* 5.7 0.2 - - - -
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Residues in contact with GLY 940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B 666 3.4 21.9 - - - +
736B TYR* 5.7 0.2 + - - -
938B ILE 3.3 3.6 - - - -
939B ASN* 1.3 85.4 - - - +
941B PRO* 1.3 62.3 - - - +
942B ALA 2.9 6.6 + - - -
943B LYS* 3.0 19.8 + - - +
948B HIS* 3.6 11.3 - - - +
951B TRP* 4.5 13.0 - - - -
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Residues in contact with PRO 941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B 666 3.2 32.7 - - + +
938B ILE 3.7 2.0 - - - +
940B GLY* 1.3 84.2 - - - +
942B ALA* 1.3 55.5 + - - +
943B LYS 3.3 2.0 - - - -
948B HIS* 3.6 17.9 - - + +
991B PHE* 5.3 0.2 - - + -
992B ILE* 3.8 30.7 - - + -
996B VAL* 3.7 33.4 - - + -
1065B LEU* 3.2 20.9 - - + -
1068B ASN* 2.9 20.3 + - + +
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Residues in contact with ALA 942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B TRP* 2.8 33.3 + - + -
935B LEU* 5.6 3.6 - - + -
939B ASN* 2.8 20.7 + - + +
941B PRO* 1.3 73.9 - - - +
943B LYS* 1.3 56.1 + - - +
996B VAL* 5.2 2.5 - - + -
1000B CYS* 4.9 4.5 - - - -
1061B LEU* 3.6 37.9 - - + +
1064B HIS* 3.4 14.3 - - - +
1065B LEU* 4.1 10.8 - - + +
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Residues in contact with LYS 943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B TRP* 3.4 60.9 + - + +
678B ASN* 3.5 8.5 - - - +
679B PHE* 5.5 2.2 + - - +
744B ASP* 3.2 26.3 + - - -
747B HIS* 4.7 8.4 + - - -
748B ALA* 5.2 1.3 - - - +
939B ASN* 3.3 35.1 + - - +
940B GLY* 3.0 10.8 + - - +
942B ALA* 1.3 79.1 - - - +
944B VAL* 1.3 62.1 + - - +
947B LEU* 3.9 29.1 - - + +
951B TRP* 5.6 1.9 - - + +
1064B HIS* 3.2 9.6 - - - +
1068B ASN* 2.9 24.3 + - - -
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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