Contacts of the helix formed by residues 958 - 968 (chain C) in PDB entry 6M6C
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 958 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956C GLY 5.5 1.3 - - - +
957C LYS* 1.3 77.4 - - - +
959C PRO* 1.3 75.4 - - - +
960C GLU* 3.7 8.0 + - - +
961C GLU* 2.5 43.8 + - - +
962C GLN* 3.1 18.1 + - - +
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Residues in contact with PRO 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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936C VAL* 4.0 33.2 - - + -
941C VAL* 4.8 11.2 - - + -
944C LEU* 3.4 27.4 - - + +
957C LYS 3.9 1.5 - - - +
958C THR* 1.3 87.6 - - - +
960C GLU* 1.3 56.8 + - - +
962C GLN* 4.3 4.0 - - - +
963C LEU* 2.9 28.6 + - - +
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Residues in contact with GLU 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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922C PHE* 4.1 10.5 - - + -
926C PHE* 3.5 42.4 - - + -
930C LYS* 5.7 5.6 - - - +
936C VAL* 4.8 2.8 - - + +
958C THR* 3.1 8.7 + - - +
959C PRO* 1.3 79.1 - - - +
961C GLU* 1.3 62.3 + - + +
963C LEU* 3.3 8.1 + - - +
964C LYS* 2.9 27.9 + - + +
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Residues in contact with GLU 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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957C LYS* 3.3 27.6 - - + +
958C THR* 2.5 52.4 + - - +
960C GLU* 1.3 81.2 - - + +
962C GLN* 1.3 58.5 + - - +
964C LYS* 3.3 9.5 + - - +
965C GLU* 2.9 32.0 + - - +
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Residues in contact with GLN 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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944C LEU* 3.7 34.3 - - + +
948C GLU* 3.6 18.9 + - - +
953C VAL* 3.5 25.4 - - + +
954C THR 3.1 26.9 + - - +
955C PRO* 4.2 2.0 - - - +
956C GLY 4.6 1.0 - - - +
957C LYS* 3.9 22.8 + - + +
958C THR 3.1 10.2 + - - +
959C PRO* 3.8 9.8 - - - +
961C GLU* 1.3 75.0 - - - +
963C LEU* 1.3 60.0 + - - +
965C GLU* 3.2 8.5 + - - +
966C LEU* 2.9 32.1 + - - +
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Residues in contact with LEU 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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922C PHE* 4.3 11.7 - - + -
925C TYR* 5.7 9.4 - - + +
926C PHE* 4.0 26.0 - - + -
929C ARG* 4.4 1.1 - - - +
936C VAL* 4.2 18.6 - - + -
940C GLU* 4.3 21.5 - - + +
944C LEU* 4.4 16.1 - - + +
959C PRO 2.9 16.4 + - - +
960C GLU* 3.5 5.6 - - - +
962C GLN* 1.3 75.8 - - - +
964C LYS* 1.3 57.8 + - - +
966C LEU* 3.3 9.1 + - + +
967C PHE* 2.9 28.9 + - - +
971C LYS 6.2 0.2 - - - +
972C VAL* 6.0 2.5 - - - -
973C VAL* 4.1 27.6 - - + +
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Residues in contact with LYS 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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919C ALA* 4.3 22.7 - - - +
922C PHE* 3.5 43.0 - - + -
923C GLU* 3.4 18.2 + - - +
960C GLU* 2.9 11.8 + - + +
961C GLU* 3.5 11.0 - - - +
963C LEU* 1.3 73.8 - - - +
965C GLU* 1.3 59.3 + - - +
967C PHE* 3.2 2.6 + - - +
968C LEU* 2.9 47.8 + - + +
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Residues in contact with GLU 965 (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 LEU 4.6 0.7 - - - +
953C VAL* 3.4 11.9 - - + +
954C THR* 3.0 43.3 + - - +
957C LYS* 2.4 38.0 + - - +
961C GLU 2.9 18.7 + - - +
962C GLN* 3.2 7.4 + - - +
964C LYS* 1.3 76.8 - - + +
966C LEU* 1.3 61.8 + - - +
968C LEU* 3.6 11.9 + - + +
969C GLN* 3.1 29.3 + - - +
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Residues in contact with LEU 966 (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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943C VAL* 5.4 1.8 - - + -
944C LEU* 3.8 26.5 - - + -
947C ALA* 4.5 6.7 - - + -
952C LEU* 4.0 18.8 - - + -
953C VAL* 3.7 23.8 - - + -
962C GLN 2.9 8.2 + - - +
963C LEU* 3.6 12.1 - - + +
965C GLU* 1.3 75.6 - - - +
967C PHE* 1.3 64.7 + - - +
969C GLN* 3.1 19.9 + - - +
970C GLY 3.6 0.2 + - - -
971C LYS* 3.1 30.0 + - + +
972C VAL* 6.1 0.2 - - - -
973C VAL* 4.9 10.8 - - + -
986C PRO* 3.9 38.4 - - + -
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Residues in contact with PHE 967 (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 LEU* 4.0 18.1 - - + +
896C PHE* 4.2 21.8 - + - -
918C LEU* 3.2 49.4 - - + +
921C ALA* 4.3 4.5 - - + -
922C PHE* 3.4 37.2 - + + -
925C TYR* 4.0 20.4 - + - -
963C LEU 2.9 18.0 + - - +
964C LYS 3.2 4.5 + - - +
966C LEU* 1.3 76.0 - - - +
968C LEU* 1.3 58.5 - - + +
969C GLN 3.0 0.2 - - - -
970C GLY* 2.8 20.8 + - - +
971C LYS 3.5 7.3 + - - +
972C VAL* 3.6 28.7 - - + -
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Residues in contact with LEU 968 (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 LYS* 3.4 47.5 + - + +
918C LEU* 3.8 15.5 - - + +
919C ALA* 3.5 41.1 - - + +
964C LYS* 2.9 32.9 + - + +
965C GLU* 3.9 9.4 - - + +
966C LEU 3.3 0.6 - - - -
967C PHE* 1.3 77.6 - - + +
969C GLN* 1.3 59.4 + - + +
970C GLY 3.4 0.4 - - - -
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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