Contacts of the helix formed by residues 942 - 951 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A CYS* 3.4 6.7 - - - -
729A LEU* 3.4 34.1 - - + +
730A CYS* 3.5 1.6 - - + -
744A HIS* 3.9 8.7 - - + -
745A SER 3.7 37.5 - - - -
746A ILE* 3.8 6.8 - - + +
937A HIS* 4.3 1.8 - - - -
938A LYS* 2.9 21.9 + - + +
941A ALA* 1.3 84.3 + - + +
943A VAL* 1.3 66.6 + - - +
944A PRO* 3.4 2.5 - - - -
945A GLU* 3.5 13.8 + - - -
946A ILE* 2.9 30.2 + - + +
1101A ZN 2.1 36.7 - - - -
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Residues in contact with VAL 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A ILE* 5.1 3.4 - - + -
796A CYS* 4.8 9.4 - - - -
892A VAL* 4.0 19.1 - - + -
893A TRP* 4.6 13.2 - - + -
909A TYR* 3.2 44.0 - - + +
938A LYS 3.3 2.9 + - - +
939A THR* 3.3 23.5 + - + +
942A HIS* 1.3 78.5 - - - +
944A PRO* 1.3 64.8 - - + +
946A ILE* 3.7 5.0 - - - +
947A ILE* 2.9 36.8 + - + +
953A ILE* 4.9 9.0 - - + -
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Residues in contact with PRO 944 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A LEU* 5.1 10.8 - - + +
909A TYR* 3.3 32.8 - - + -
910A SER* 4.5 17.0 - - - +
913A SER* 5.9 0.4 - - - +
940A LEU 5.5 1.6 - - - +
941A ALA 4.7 5.4 - - - +
942A HIS* 3.7 4.5 - - - +
943A VAL* 1.3 95.4 - - + +
945A GLU* 1.3 58.7 + - + +
947A ILE* 3.4 7.1 + - + +
948A GLU* 3.0 30.5 + - - +
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Residues in contact with GLU 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A HIS 2.9 27.2 - - - +
745A SER* 3.2 9.9 + - - -
746A ILE* 2.9 47.1 + - + +
941A ALA 3.4 13.3 - - - +
942A HIS* 3.5 6.8 + - - +
943A VAL 3.3 0.6 - - - -
944A PRO* 1.3 77.4 - - + +
946A ILE* 1.3 59.3 + - - +
948A GLU* 3.4 20.5 + - - +
949A ARG* 2.9 28.8 + - - +
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Residues in contact with ILE 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A LEU* 3.9 17.7 - - + -
746A ILE* 4.1 13.9 - - + -
790A SER* 3.8 21.8 - - - +
791A ILE* 4.3 21.1 - - + -
938A LYS* 5.4 4.7 - - + +
942A HIS* 2.9 28.5 + - + +
943A VAL* 3.8 3.1 - - - +
945A GLU* 1.3 73.1 - - - +
947A ILE* 1.3 60.9 + - - +
949A ARG* 3.2 18.8 + - - +
950A ASP* 2.9 44.4 + - - +
952A SER 4.5 2.6 - - - +
953A ILE* 3.6 21.1 - - + -
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Residues in contact with ILE 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A VAL* 3.9 24.9 - - + +
898A PRO* 3.6 28.3 - - + -
899A ALA* 6.2 0.7 - - + -
906A LEU* 3.7 33.0 - - + -
943A VAL* 2.9 22.9 + - + +
944A PRO 3.7 4.3 - - - +
946A ILE* 1.3 75.1 - - - +
948A GLU* 1.3 60.2 + - - +
951A GLY* 2.4 40.9 + - - +
952A SER* 3.9 10.3 - - - +
953A ILE* 3.6 27.1 - - + -
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Residues in contact with GLU 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A PRO 3.0 14.2 + - - +
945A GLU* 3.5 24.0 - - - +
947A ILE* 1.3 78.8 - - - +
949A ARG* 1.3 63.9 + - + +
951A GLY 4.8 0.2 + - - -
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Residues in contact with ARG 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ARG* 3.1 18.7 + - - +
729A LEU* 4.8 3.8 - - - +
746A ILE* 4.3 26.1 - - + +
788A VAL* 3.4 27.6 - - - +
789A PRO* 2.7 34.6 + - - +
790A SER* 3.8 3.4 - - - +
945A GLU 2.9 17.9 + - - +
946A ILE* 3.6 23.1 - - - +
947A ILE 3.1 0.2 - - - -
948A GLU* 1.3 81.9 - - + +
950A ASP* 1.3 84.9 + - - +
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Residues in contact with ASP 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A ARG* 4.3 16.3 + - - -
703A ARG* 2.3 42.1 + - - +
705A THR* 5.0 1.7 - - - +
788A VAL* 4.4 2.0 - - - +
790A SER* 4.2 8.1 + - - -
946A ILE* 2.9 18.6 + - - +
949A ARG* 1.3 110.4 + - - +
951A GLY* 1.3 58.6 + - - +
952A SER* 3.2 18.8 + - - +
956A TRP* 3.9 25.4 + - + +
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Residues in contact with GLY 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897A CYS* 4.5 7.7 - - - -
898A PRO* 3.1 24.8 - - - +
899A ALA* 4.7 5.4 + - - +
947A ILE* 2.4 34.3 + - - +
948A GLU 4.5 0.8 + - - -
949A ARG 3.8 0.6 - - - -
950A ASP* 1.3 66.8 - - - +
952A SER* 1.3 57.6 + - - +
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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