Contacts of the strand formed by residues 947 - 954 (chain C) in PDB entry 3KBU
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 THR 947 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1792B LEU* 5.0 1.6 - - - -
918C MET* 3.6 7.1 - - - +
919C VAL* 2.8 31.7 + - - +
943C CYS* 3.5 17.5 - - - -
945C ALA* 2.8 20.5 + - - +
946C PRO* 1.3 75.6 + - - +
948C ARG* 1.3 64.6 + - - +
949C ILE* 3.6 25.9 + - + -
980C PRO* 4.2 15.7 - - + -
983C ALA* 5.9 2.7 - - + -
985C PHE* 5.7 1.6 - - + -
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Residues in contact with ARG 948 (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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1710B GLU 5.3 0.4 + - - -
1713B ALA* 3.5 28.1 + - - +
1714B SER* 4.1 17.2 + - - +
1715B SER 5.7 0.2 + - - -
1785B LEU* 3.2 43.4 + - - +
1788B THR* 2.9 23.0 + - - +
1789B ARG* 3.5 20.6 - - - +
1792B LEU* 4.0 22.9 - - + +
916C SER* 3.7 13.9 - - - +
917C PHE 3.7 4.3 - - - +
918C MET* 3.7 14.8 - - - +
947C THR* 1.3 73.9 - - - +
949C ILE* 1.3 59.0 + - - +
950C THR* 3.8 17.0 + - + +
952C ARG* 5.7 0.4 - - - +
979C GLY 3.8 0.9 - - - +
980C PRO* 3.6 20.4 - - - +
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Residues in contact with ILE 949 (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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916C SER* 2.9 19.9 + - - -
917C PHE* 2.9 52.3 + - + +
919C VAL* 3.8 23.3 - - + -
936C VAL* 4.9 4.7 - - + -
938C ILE* 3.8 21.3 - - + -
947C THR* 3.8 18.8 - - + -
948C ARG* 1.3 72.2 - - - +
950C THR* 1.3 70.4 + - - +
951C CYS* 5.2 2.7 - - + -
978C LEU* 5.6 1.6 - - + -
979C GLY 3.1 6.3 - - - +
980C PRO* 4.6 1.1 - - + -
985C PHE* 4.2 6.5 - - + -
1059C PHE* 3.8 29.6 - - + -
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Residues in contact with THR 950 (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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1785B LEU* 3.9 15.7 - - + -
915C VAL 3.1 7.0 - - - -
916C SER* 3.8 11.2 - - - +
917C PHE* 6.0 0.2 - - - -
948C ARG* 3.8 26.9 - - - +
949C ILE* 1.3 82.9 - - - +
951C CYS* 1.3 64.5 + - - +
952C ARG* 4.2 22.0 + - - +
977C ALA 4.1 1.8 + - - -
978C LEU* 3.3 4.5 - - - +
979C GLY* 2.8 45.2 + - - +
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Residues in contact with CYS 951 (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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913C PHE* 4.2 15.9 - - + -
914C LEU 4.4 1.7 - - - +
915C VAL* 2.8 29.4 + - - +
917C PHE* 5.5 1.1 - - + -
934C LEU* 3.8 36.3 - - - -
936C VAL* 5.0 5.4 - - + -
949C ILE* 5.2 3.6 - - + -
950C THR* 1.3 78.5 - - - +
952C ARG* 1.3 61.7 + - - +
953C LEU* 4.9 3.7 - - - +
976C ILE* 4.6 8.5 - - - -
977C ALA 3.4 4.7 - - - -
978C LEU* 3.4 26.7 - - + -
993C ILE* 5.6 1.3 - - - -
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Residues in contact with ARG 952 (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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1710B GLU* 3.0 32.5 + - - +
1714B SER* 5.5 8.7 - - - -
1785B LEU* 3.4 32.8 - - - +
915C VAL* 4.5 17.7 - - + +
948C ARG* 5.7 0.2 - - - +
950C THR* 4.2 19.3 + - - +
951C CYS* 1.3 78.8 - - - +
953C LEU* 1.3 65.4 + - - +
954C VAL* 3.8 17.7 + - + -
975C ILE 3.4 2.6 - - - +
976C ILE* 3.6 3.3 - - - +
977C ALA* 3.0 42.3 + - + +
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Residues in contact with LEU 953 (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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931C HIS* 4.3 26.2 - - + +
934C LEU* 3.5 32.5 - - + -
951C CYS* 4.9 5.8 - - - +
952C ARG* 1.3 81.1 - - - +
954C VAL* 1.3 62.1 + - - +
974C ARG* 3.6 39.5 + - + +
975C ILE 3.3 3.6 - - - -
976C ILE* 3.9 20.0 - - + -
993C ILE* 5.8 2.0 - - + -
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Residues in contact with VAL 954 (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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952C ARG* 4.2 23.3 - - + +
953C LEU* 1.3 76.9 - - - +
955C LYS* 1.3 74.6 + - - +
958C LYS* 3.7 21.3 - - + -
959C LEU* 3.9 17.5 - - + -
974C ARG* 3.6 4.2 - - - +
975C ILE* 2.9 41.7 + - + +
977C ALA* 4.7 11.0 - - + -
1062C TYR* 5.4 4.5 - - + +
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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