Contacts of the helix formed by residues 939 - 943 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677K TRP* 4.2 20.4 - - + -
744K ASP* 3.5 20.7 + - - +
745K VAL* 4.9 1.4 - - - +
748K ALA* 4.2 8.0 - - - +
935K LEU* 3.1 18.6 + - + +
936K ALA* 2.7 23.3 - - - +
937K ASP 3.5 1.6 + - - +
938K ILE* 1.3 77.3 - - - +
940K GLY* 1.3 72.2 + - - +
941K PRO 3.4 0.4 - - - -
942K ALA* 2.7 24.4 + - - +
943K LYS* 3.1 42.3 + - - +
951K TRP* 5.2 0.6 - - - +
996K VAL* 5.8 0.9 - - - -
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Residues in contact with GLY 940 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938K ILE* 3.1 5.5 - - - +
939K ASN* 1.3 85.8 - - - +
941K PRO* 1.3 61.6 - - - +
942K ALA 3.0 3.6 + - - -
943K LYS* 3.2 18.0 + - - +
948K HIS* 3.5 17.9 + - - +
951K TRP* 4.7 18.3 - - - -
2121K IBM 3.9 13.0 - - - -
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Residues in contact with PRO 941 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938K ILE 3.7 7.4 - - - +
940K GLY* 1.3 83.6 - - - +
942K ALA* 1.3 58.3 + - - +
943K LYS 3.4 1.1 - - - -
948K HIS* 3.3 31.6 - - + +
991K PHE* 4.6 2.7 - - + -
992K ILE* 3.9 27.1 - - + -
996K VAL* 3.8 26.2 - - + -
1065K LEU* 3.2 25.0 - - + -
1068K ASN* 2.9 19.5 + - + +
2121K IBM 3.8 15.9 - - - +
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Residues in contact with ALA 942 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677K TRP* 3.0 24.0 + - + -
935K LEU* 5.6 2.0 - - + -
939K ASN* 2.7 23.1 + - - +
941K PRO* 1.3 72.8 - - - +
943K LYS* 1.3 59.2 + - - +
996K VAL* 5.3 2.2 - - + -
1000K CYS* 4.9 5.2 - - - -
1061K LEU* 3.5 39.2 - - + +
1064K HIS* 3.2 14.6 - - - +
1065K LEU* 4.0 11.4 - - + +
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Residues in contact with LYS 943 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677K TRP* 3.3 56.2 + - + +
678K ASN* 3.5 7.4 - - - +
679K PHE* 5.0 3.6 + - - +
681K ILE* 6.2 0.8 - - - +
744K ASP* 3.2 26.2 + - - -
747K HIS* 5.0 6.1 + - - -
748K ALA* 5.7 1.1 - - - -
939K ASN* 3.1 29.4 - - - +
940K GLY* 3.2 13.1 + - - +
942K ALA* 1.3 79.3 - - - +
944K VAL* 1.3 71.6 + - - +
947K LEU* 4.0 29.2 - - + +
951K TRP* 5.0 4.4 - - + +
1064K HIS* 3.3 11.3 + - - +
1068K 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