Contacts of the helix formed by residues 950 - 964 (chain C) in PDB entry 3KKA
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 LEU 950 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920C TYR* 4.0 6.2 + - - +
948C VAL* 4.3 0.4 - - - +
949C ARG* 1.3 78.7 - - + +
951C PRO* 1.4 71.4 - - + +
952C GLY 3.3 0.9 - - - +
953C HIS* 3.1 44.7 + - + +
954C GLN* 2.9 26.4 + - - +
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Residues in contact with PRO 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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949C ARG 3.4 6.9 - - - +
950C LEU* 1.4 88.4 - - + +
952C GLY* 1.3 58.4 + - - +
954C GLN* 3.2 18.6 + - - +
955C LYS* 2.9 30.7 + - - +
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Residues in contact with GLY 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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950C LEU* 3.3 1.4 - - - +
951C PRO* 1.3 80.2 - - - +
953C HIS* 1.3 64.4 + - - +
955C LYS* 3.2 12.5 + - - +
956C ARG* 3.0 25.7 + - - +
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Residues in contact with HIS 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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917C MET* 3.6 29.5 - - + +
919C GLN* 3.4 13.1 + - - -
920C TYR* 2.8 32.5 - + + +
948C VAL* 3.8 15.5 - - + -
950C LEU* 3.1 35.8 + - + +
952C GLY* 1.3 77.0 - - - +
954C GLN* 1.3 61.2 + - - +
956C ARG* 3.6 2.5 + - - +
957C ILE* 3.1 30.1 + - - +
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Residues in contact with GLN 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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940C ASN* 4.6 6.6 + - - +
943C ILE* 4.3 17.8 - - + +
944C LYS* 3.2 34.2 - - + +
948C VAL* 2.8 37.9 + - + +
949C ARG 3.4 17.5 + - - +
950C LEU 2.9 10.2 + - - +
951C PRO* 3.2 18.8 + - - +
953C HIS* 1.3 75.9 - - - +
955C LYS* 1.3 57.2 + - - +
957C ILE* 4.2 0.9 - - - +
958C ALA* 2.9 31.8 + - - +
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Residues in contact with LYS 955 (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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940C ASN* 6.0 0.2 - - - +
951C PRO 2.9 13.8 + - - +
952C GLY* 3.4 15.5 - - - +
954C GLN* 1.3 74.7 - - - +
956C ARG* 1.3 60.4 + - - +
958C ALA* 3.2 5.1 + - + +
959C TYR* 2.9 62.4 + - + +
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Residues in contact with ARG 956 (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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915C ILE* 3.0 45.8 + - + +
916C LYS* 4.3 13.3 + - - +
917C MET* 4.0 17.5 - - + +
952C GLY 3.0 15.9 + - - +
953C HIS* 4.0 4.3 - - - +
955C LYS* 1.3 76.0 - - - +
957C ILE* 1.3 58.6 + - - +
959C TYR* 3.4 4.6 + - - +
960C SER* 2.9 29.9 + - - -
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Residues in contact with ILE 957 (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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911C TRP* 3.6 26.2 - - + -
912C LEU* 4.4 1.3 - - + -
915C ILE* 3.9 11.9 - - + -
917C MET* 3.9 31.2 - - + -
920C TYR* 4.3 8.3 - - + -
924C PHE* 4.2 17.0 - - + -
938C MET* 4.9 0.7 - - + -
943C ILE* 4.2 19.3 - - + -
948C VAL* 3.9 30.7 - - + -
953C HIS 3.1 18.5 + - - +
954C GLN 4.3 1.8 - - - +
956C ARG* 1.3 72.3 - - - +
958C ALA* 1.3 56.3 + - - +
960C SER* 3.2 0.7 + - - -
961C LEU* 2.6 39.0 + - + +
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Residues in contact with ALA 958 (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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940C ASN* 3.4 33.5 - - - +
943C ILE* 3.9 11.9 - - + +
954C GLN 2.9 24.4 + - - +
955C LYS* 3.2 7.6 + - - +
957C ILE* 1.3 74.4 - - - +
959C TYR* 1.3 59.2 + - + +
961C LEU* 3.4 6.1 - - - +
962C LEU* 3.1 31.9 + - + +
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Residues in contact with TYR 959 (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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955C LYS* 2.9 54.5 + - + +
956C ARG* 4.0 4.3 - - - +
958C ALA* 1.3 73.1 - - + +
960C SER* 1.3 67.0 + - - +
961C LEU 3.1 0.9 - - - -
962C LEU* 3.2 24.1 + - + +
963C GLY* 3.1 18.7 + - - -
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Residues in contact with SER 960 (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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911C TRP* 3.6 14.9 + - - -
915C ILE* 2.9 44.1 - - - +
956C ARG* 2.9 18.8 + - - -
957C ILE 3.5 4.0 - - - -
959C TYR* 1.3 75.1 - - - +
961C LEU* 1.3 61.1 + - - +
963C GLY* 3.1 12.5 + - - -
964C LEU* 3.4 15.8 + - - +
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Residues in contact with LEU 961 (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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911C TRP* 4.3 12.3 - - + +
935C VAL* 3.1 36.6 - - + +
936C VAL* 4.4 7.2 - - - -
938C MET* 3.8 31.4 - - + +
939C THR* 5.3 2.0 - - - -
940C ASN* 5.4 4.3 - - - +
943C ILE* 4.8 10.1 - - + -
957C ILE* 2.6 22.0 + - + +
958C ALA* 3.4 10.1 - - - +
959C TYR 3.1 0.2 - - - -
960C SER* 1.3 72.9 - - - +
962C LEU* 1.3 66.3 + - + +
964C LEU* 3.2 24.3 + - + +
965C LYS* 3.8 23.9 - - - +
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Residues in contact with LEU 962 (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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958C ALA* 3.1 19.1 + - + +
959C TYR* 3.2 29.8 + - + +
961C LEU* 1.3 80.0 - - + +
963C GLY* 1.3 61.0 + - - +
964C LEU 3.5 0.2 + - - -
965C LYS* 3.6 32.6 + - + +
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Residues in contact with GLY 963 (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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959C TYR 3.1 12.2 + - - -
960C SER* 3.1 7.1 + - - -
962C LEU* 1.3 78.6 - - - +
964C LEU* 1.3 58.3 + - - +
965C LYS 3.2 8.6 + - - +
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Residues in contact with LEU 964 (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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911C TRP* 3.5 44.6 - - + +
932C ILE* 4.6 16.2 - - + -
935C VAL* 4.3 17.0 - - + -
936C VAL* 3.9 20.2 - - + +
960C SER 3.4 8.0 + - - +
961C LEU* 3.2 15.2 + - + +
963C GLY* 1.3 75.2 - - - +
965C LYS* 1.3 67.8 + - - +
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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