Contacts of the helix formed by residues 939 - 950 (chain C) in PDB entry 1X86
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 LYS 939 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935C GLN* 3.1 23.1 - - - +
936C ARG* 2.6 22.6 + - - +
938C THR* 1.3 71.9 - - - +
940C TYR* 1.3 65.8 + - - +
941C PRO* 3.2 2.9 - - - -
942C LEU* 2.9 26.2 + - + +
943C LEU* 3.2 16.5 + - + +
37D THR 3.6 15.9 + - - +
38D VAL* 4.1 33.0 - - + +
39D PHE 3.7 17.1 - - - +
59D ASP* 3.5 26.7 + - - +
61D ALA* 3.4 31.4 + - - +
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Residues in contact with TYR 940 (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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795C LEU* 4.1 18.6 - - + -
799C GLU* 2.4 30.8 + - - -
842C HIS* 3.1 28.5 - + - -
845C LEU* 4.2 2.8 - - + +
849C MET* 5.2 0.7 - - + -
872C PHE* 3.8 35.9 - + + -
880C LEU* 4.5 9.0 - - + -
936C ARG* 3.3 32.7 + - + -
937C LEU* 4.0 26.5 - - + +
939C LYS* 1.3 77.9 - - - +
941C PRO* 1.3 65.0 - - + +
943C LEU* 3.1 4.6 + - + -
944C LEU* 2.8 35.4 + - + +
967C CYS* 3.9 19.3 - - + -
970C ILE* 6.0 1.3 - - + -
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Residues in contact with PRO 941 (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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937C LEU 3.3 11.0 - - - +
938C THR 3.6 7.9 - - - +
939C LYS 3.3 4.7 - - - -
940C TYR* 1.3 95.5 - - + +
942C LEU* 1.3 58.6 + - + +
944C LEU* 4.4 5.6 - - + -
945C ASP* 2.7 37.2 + - - +
964C ALA 4.4 3.6 - - - +
967C CYS* 3.8 16.2 - - + +
968C ARG* 3.5 32.3 - - + +
971C LEU* 3.3 26.2 - - + -
66D TYR* 5.3 0.7 - - + +
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Residues in contact with LEU 942 (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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938C THR 4.0 8.1 - - - +
939C LYS* 2.9 20.4 + - + +
941C PRO* 1.3 78.9 - - + +
943C LEU* 1.3 58.8 + - - +
945C ASP* 3.3 11.6 + - - +
946C ASN* 2.9 35.5 + - - +
968C ARG* 5.5 1.8 - - - +
37D THR* 3.3 28.5 - - + +
61D ALA* 3.7 27.1 - - + +
62D GLY* 3.8 18.6 - - - +
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Residues in contact with LEU 943 (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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791C VAL* 3.9 15.4 - - + +
794C GLU* 4.0 30.7 - - + +
795C LEU* 4.3 25.8 - - + +
798C THR* 5.5 0.2 - - - +
936C ARG* 4.3 11.7 - - - +
939C LYS* 3.3 32.1 - - + +
940C TYR* 3.1 9.3 + - - +
942C LEU* 1.3 74.7 - - - +
944C LEU* 1.3 61.1 + - + +
946C ASN* 3.1 5.2 + - - +
947C ILE* 2.6 38.9 + - + +
37D THR* 3.7 24.9 - - + -
38D VAL* 4.1 8.5 - - + -
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Residues in contact with LEU 944 (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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795C LEU* 4.0 31.4 - - + -
868C LEU* 4.1 18.2 - - + -
872C PHE* 3.8 17.9 - - + -
940C TYR* 2.8 20.3 + - - +
941C PRO 4.0 1.1 - - - +
943C LEU* 1.3 76.9 - - + +
945C ASP* 1.3 67.0 + - - +
947C ILE* 4.2 7.2 - - + -
948C ALA* 3.1 14.0 + - - +
960C VAL* 3.4 14.7 - - + +
963C ALA* 3.8 16.6 - - + +
964C ALA* 3.9 18.8 - - + +
967C CYS* 3.7 30.1 - - + -
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Residues in contact with ASP 945 (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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941C PRO 2.7 23.0 + - - +
942C LEU* 3.4 11.6 - - - +
944C LEU* 1.3 72.7 - - - +
946C ASN* 1.3 58.9 + - - +
948C ALA* 2.5 32.7 + - - +
949C LYS* 2.8 12.0 + - - -
964C ALA* 3.6 15.1 - - - +
968C ARG* 2.6 29.8 + - - -
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Residues in contact with ASN 946 (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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791C VAL* 4.1 18.8 - - + -
942C LEU* 2.9 25.7 + - - +
943C LEU 3.5 5.2 - - - +
945C ASP* 1.3 76.0 - - - +
947C ILE* 1.3 65.6 + - - +
949C LYS* 2.8 34.6 + - - +
950C TYR* 3.1 27.0 + - + -
37D THR* 3.3 25.3 + - - +
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Residues in contact with ILE 947 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788C ARG* 4.0 15.7 - - + +
791C VAL* 3.9 18.3 - - + +
792C ILE* 3.6 37.0 - - + +
795C LEU* 3.6 30.3 - - + -
864C ILE* 4.6 11.4 - - + -
868C LEU* 4.7 6.1 - - + -
943C LEU 2.6 21.0 + - - +
944C LEU* 3.8 15.7 - - + +
946C ASN* 1.3 72.9 - - - +
948C ALA* 1.3 53.1 + - - +
950C TYR* 3.7 3.9 + - - -
951C THR* 2.3 28.7 + - - +
960C VAL* 3.7 22.2 - - + -
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Residues in contact with ALA 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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944C LEU 3.1 13.2 + - - +
945C ASP* 2.5 23.7 + - - +
947C ILE* 1.3 73.1 - - - +
949C LYS* 1.3 62.0 + - - -
951C THR* 3.2 11.3 + - - -
957C ARG* 3.0 30.1 - - + -
960C VAL* 3.8 19.3 - - + -
961C LYS* 4.1 23.8 - - + +
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Residues in contact with LYS 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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945C ASP 2.8 13.4 + - - +
946C ASN* 2.8 26.9 + - - +
948C ALA* 1.3 71.3 - - - +
950C TYR* 1.3 94.3 + - + +
951C THR 3.8 1.4 + - - -
957C ARG* 5.3 1.6 - - - -
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Residues in contact with TYR 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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784C CYS* 3.6 45.8 - - + +
785C GLU* 4.6 3.5 - - - +
787C LYS* 3.7 44.0 - - + +
788C ARG* 3.5 27.0 - - + +
791C VAL* 4.4 10.8 - - + -
946C ASN* 3.1 37.8 + - + -
947C ILE 4.0 0.9 - - - +
948C ALA 3.2 0.6 - - - -
949C LYS* 1.3 112.0 + - + +
951C THR* 1.3 60.2 + - - +
952C GLU* 3.6 3.8 + - - +
34D TYR* 6.2 1.0 - + - -
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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