Contacts of the helix formed by residues 943 - 950 (chain O) in PDB entry 6IY3
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 PRO 943 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685O GLN* 4.0 18.6 + - - +
686O THR* 5.6 7.9 - - + -
787O ASN* 3.9 11.2 - - - +
919O ARG* 5.5 5.6 - - - +
939O ASN 4.0 0.2 - - - +
940O PHE 4.8 2.9 - - - +
941O VAL 3.6 8.7 - - - +
942O LEU* 1.3 83.6 - - + +
944O LYS* 1.3 62.6 + - - +
945O ILE 3.3 0.4 - - - -
946O PHE* 3.2 38.7 - - + +
947O ASN* 4.5 7.3 + - - -
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Residues in contact with LYS 944 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675O LYS* 3.9 11.3 + - - +
678O ARG* 3.4 41.7 - - + +
679O ILE* 3.7 32.1 - - + +
682O LEU* 3.6 38.8 - - + +
685O GLN* 4.6 10.1 + - - +
942O LEU* 3.2 3.0 - - + +
943O PRO* 1.3 79.2 - - - +
945O ILE* 1.3 85.3 + - + +
946O PHE 3.2 1.4 + - - -
947O ASN* 3.2 8.6 + - - +
948O SER* 3.1 35.0 + - - -
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Residues in contact with ILE 945 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675O LYS* 6.5 0.4 - - + -
679O ILE* 5.4 0.4 - - + -
937O LEU 4.6 3.4 - - - +
938O LEU* 3.1 44.2 - - + +
942O LEU* 3.2 33.9 + - + +
944O LYS* 1.3 104.6 - - + +
946O PHE* 1.3 66.9 + - - +
948O SER* 3.2 5.2 - - - +
949O VAL* 2.9 38.7 + - + -
950O LYS 3.9 1.0 + - - -
986O VAL* 6.4 1.6 - - + -
990O PHE* 4.6 20.6 - - + -
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Residues in contact with PHE 946 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911O ASN* 4.3 21.3 - - - -
938O LEU 3.5 1.8 + - - -
939O ASN* 3.1 61.7 - - + +
940O PHE* 4.5 5.4 - - - -
942O LEU 4.2 0.8 + - - -
943O PRO* 3.2 38.1 - - + +
945O ILE* 1.3 80.8 - - - +
947O ASN* 1.3 66.9 + - - +
948O SER 3.1 1.2 + - - -
950O LYS* 3.0 54.6 + - - +
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Residues in contact with ASN 947 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682O LEU* 5.9 8.9 - - + +
943O PRO 4.6 9.5 + - - -
944O LYS* 3.2 8.8 + - - +
946O PHE* 1.3 82.9 - - - +
948O SER* 1.3 60.4 + - - +
950O LYS* 5.5 4.8 + - - +
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Residues in contact with SER 948 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675O LYS* 4.9 11.9 - - - +
678O ARG* 5.4 8.1 - - - -
944O LYS* 3.1 27.4 + - - -
945O ILE* 3.2 21.1 - - - +
947O ASN* 1.3 82.5 - - - +
949O VAL* 1.3 72.5 + - - +
950O LYS 3.6 1.5 + - - -
951O SER* 4.2 3.5 + - - -
952O PHE* 3.5 22.9 - - - -
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Residues in contact with VAL 949 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675O LYS* 3.4 37.7 - - + +
938O LEU* 3.6 40.6 - - + +
945O ILE* 2.9 22.9 + - + +
948O SER* 1.3 89.0 - - - +
950O LYS* 1.4 64.7 + - - +
951O SER 3.1 2.2 - - - +
952O PHE* 3.8 22.7 - - + +
953O ASP* 3.0 18.8 + - - +
956O PHE* 4.7 4.0 - - + -
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Residues in contact with LYS 950 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934O LEU* 6.0 1.3 - - + -
938O LEU* 5.0 2.9 - - - -
939O ASN* 3.6 16.6 - - - +
945O ILE 3.9 0.6 + - - -
946O PHE* 3.0 54.2 + - - +
947O ASN* 5.5 5.0 + - - +
948O SER 3.6 0.8 - - - -
949O VAL* 1.4 78.8 - - - +
951O SER* 1.3 55.7 + - - +
953O ASP* 3.0 22.4 - - - +
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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