Contacts of the helix formed by residues 942 - 951 (chain C) in PDB entry 6CIM
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 HIS 942 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727C CYS* 3.5 5.2 - - - -
729C LEU* 3.7 33.4 - - + +
730C CYS* 3.6 0.8 - - + -
744C HIS* 3.8 9.4 - - + -
745C SER 3.6 37.2 - - - -
746C ILE* 4.0 7.4 - - + +
937C HIS* 3.9 2.4 - - - -
938C LYS* 2.9 23.5 + - + +
941C ALA* 1.3 79.3 + - + +
943C VAL* 1.3 64.1 + - - +
944C PRO 3.5 1.8 - - - -
945C GLU* 3.4 17.4 + - - -
946C ILE* 2.9 31.5 + - + +
1101C ZN 2.0 37.4 - - - -
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Residues in contact with VAL 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 ILE* 5.0 8.7 - - + -
796C CYS* 4.9 5.4 - - - -
892C VAL* 4.3 4.3 - - + -
893C TRP* 4.3 21.1 - - + -
909C TYR* 3.5 29.4 - - + +
938C LYS 3.8 2.2 - - - +
939C THR* 3.5 35.5 + - + +
942C HIS* 1.3 77.0 - - - +
944C PRO* 1.3 71.4 - - + +
946C ILE* 3.1 7.2 + - - +
947C ILE* 2.9 40.3 + - + +
953C ILE* 4.8 3.8 - - + -
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Residues in contact with PRO 944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906C LEU* 5.3 7.9 - - + +
909C TYR* 3.4 33.7 - - + -
910C SER* 4.2 17.3 - - - +
940C LEU 5.5 0.9 - - - +
941C ALA 4.7 7.0 - - - +
942C HIS* 3.8 2.7 - - - +
943C VAL* 1.3 94.8 - - + +
945C GLU* 1.3 59.3 + - + +
947C ILE* 3.2 9.1 + - + +
948C GLU* 2.9 38.7 + - - +
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Residues in contact with GLU 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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744C HIS 2.8 26.9 - - - +
745C SER* 3.1 15.8 + - - -
746C ILE* 2.9 45.4 + - + +
941C ALA 3.4 9.8 - - - +
942C HIS* 3.4 12.1 + - - +
943C VAL 3.3 0.6 - - - -
944C PRO* 1.3 77.8 - - + +
946C ILE* 1.3 59.0 + - - +
948C GLU* 3.4 14.7 + - - +
949C ARG* 3.0 27.4 + - - +
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Residues in contact with ILE 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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729C LEU* 4.1 18.4 - - + -
746C ILE* 4.4 3.8 - - + -
790C SER* 3.6 14.8 - - - +
791C ILE* 4.1 30.7 - - + +
938C LYS* 5.4 3.4 - - + +
942C HIS* 2.9 39.6 + - + +
943C VAL* 3.8 3.8 - - - +
945C GLU* 1.3 74.1 - - - +
947C ILE* 1.3 62.2 + - - +
949C ARG* 3.2 19.4 + - - +
950C ASP* 2.8 48.5 + - + +
952C SER 4.6 0.8 - - - +
953C ILE* 3.9 14.8 - - + -
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Residues in contact with ILE 947 (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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892C VAL* 3.3 48.0 - - + +
898C PRO* 3.6 24.0 - - + -
899C ALA* 6.2 1.1 - - + -
906C LEU* 3.8 19.5 - - + -
943C VAL* 2.9 22.3 + - + +
944C PRO* 3.6 7.6 - - + +
946C ILE* 1.3 73.2 - - - +
948C GLU* 1.3 62.5 + - - +
951C GLY* 2.6 47.3 + - - +
952C SER 4.6 0.4 - - - +
953C ILE* 4.0 17.5 - - + +
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Residues in contact with GLU 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 PRO* 2.9 25.0 + - + +
945C GLU* 3.7 15.1 - - - +
946C ILE 3.3 0.2 - - - -
947C ILE* 1.3 75.9 - - - +
949C ARG* 1.3 60.6 + - - +
951C GLY 4.7 0.5 + - - -
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Residues in contact with ARG 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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703C ARG* 2.8 24.8 + - - +
729C LEU* 4.8 4.0 - - - +
746C ILE* 4.1 24.5 - - + +
788C VAL* 3.3 26.4 - - - +
789C PRO* 2.8 34.8 + - - +
790C SER* 3.8 2.0 - - - +
945C GLU 3.0 17.1 + - - +
946C ILE* 3.5 23.4 - - - +
947C ILE 3.1 0.6 - - - -
948C GLU* 1.3 79.0 - - - +
950C ASP* 1.3 86.4 + - - +
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Residues in contact with ASP 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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628C ARG* 5.7 1.7 + - - -
703C ARG* 2.5 42.5 + - - +
705C THR* 5.2 1.3 - - - +
788C VAL* 4.3 3.0 - - - +
790C SER* 4.0 7.8 + - - -
946C ILE* 2.8 20.9 + - - +
949C ARG* 1.3 107.8 + - - +
951C GLY* 1.3 57.6 + - - +
952C SER* 2.9 22.7 + - - +
956C TRP* 3.6 31.2 + - + +
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Residues in contact with GLY 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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897C CYS* 4.3 6.9 - - - -
898C PRO* 3.2 23.6 - - - +
899C ALA* 5.3 1.9 + - - +
947C ILE* 2.6 36.3 + - - +
948C GLU 4.5 0.6 + - - -
949C ARG 3.8 0.6 - - - -
950C ASP* 1.3 68.2 - - - +
952C SER* 1.3 57.4 + - - +
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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