Contacts of the helix formed by residues 962 - 976 (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 GLN 962 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961C ASN* 1.3 84.0 - - + +
963C SER* 1.3 60.1 + - - +
964C GLY 3.2 0.4 + - - -
965C ASN* 4.0 13.4 + - - +
966C LYS* 4.5 9.0 + - - +
41G G 4.4 8.3 + - - +
42G T 3.8 47.1 + - - +
43G A 4.2 10.5 + - - +
19J C 6.0 1.7 - - - +
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Residues in contact with SER 963 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C GLU* 3.9 23.8 - - - +
961C ASN* 4.6 4.9 + - - +
962C GLN* 1.3 74.4 - - - +
964C GLY* 1.3 61.9 + - - +
965C ASN 3.2 0.9 - - - -
966C LYS* 3.1 14.1 + - - +
967C LEU* 2.8 33.4 + - - +
20J A 5.5 13.2 - - - -
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Residues in contact with GLY 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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602C MET* 3.8 15.6 - - - +
621C ARG* 4.4 11.0 - - - -
961C ASN* 3.0 16.1 + - - +
963C SER* 1.3 80.5 + - - +
965C ASN* 1.3 57.1 + - - +
967C LEU* 3.3 6.9 + - - +
968C PHE* 2.8 33.1 + - - +
991C HIS* 5.9 3.7 - - - -
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Residues in contact with ASN 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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602C MET* 2.8 34.3 + - - +
604C ASP 2.7 26.8 + - - +
605C VAL* 4.7 3.3 - - - +
961C ASN 4.1 3.2 + - - -
962C GLN 4.0 5.6 + - - +
963C SER 3.2 0.6 - - - -
964C GLY* 1.3 75.3 - - - +
966C LYS* 1.3 62.0 + - - +
968C PHE* 3.6 3.4 - - - +
969C ARG* 2.9 44.9 + - - +
41G G 3.5 40.2 + - - +
42G T 3.9 7.1 + - - +
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Residues in contact with LYS 966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962C GLN 4.7 10.5 - - - +
963C SER* 3.1 12.1 + - - +
965C ASN* 1.3 77.7 - - + +
967C LEU* 1.3 58.0 + - - +
969C ARG* 3.4 10.7 + - - +
970C ARG* 2.9 35.1 + - - +
39G G 4.7 12.5 - - - +
40G T 5.0 14.1 + - - -
41G G 4.8 25.6 - - - -
19J C 5.2 1.0 + - - -
20J A 3.2 44.6 + - - +
21J G 5.7 4.5 - - - +
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Residues in contact with LEU 967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C PHE* 5.6 4.0 - - + -
649C GLU* 4.8 14.4 - - + -
963C SER* 2.8 19.4 + - - +
964C GLY* 3.8 5.2 - - - +
966C LYS* 1.3 74.1 - - - +
968C PHE* 1.3 66.5 + - - +
970C ARG* 3.2 10.3 + - - +
971C PHE* 3.0 54.9 + - + -
991C HIS* 3.4 37.5 - - + +
994C TYR* 3.3 36.8 - - + +
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Residues in contact with PHE 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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602C MET* 3.3 31.6 - - + -
605C VAL* 3.4 37.7 - - + -
619C ALA* 4.5 2.7 - - + -
657C LEU* 3.9 24.2 - - + -
658C MET 5.4 0.4 - - - -
659C LEU* 4.2 12.6 - - + -
964C GLY 2.8 21.6 + - - +
965C ASN* 3.6 4.5 - - - +
967C LEU* 1.3 78.5 - - + +
969C ARG* 1.3 62.8 + - - +
971C PHE* 3.3 5.2 + - - +
972C ARG* 3.0 34.9 + - + +
984C MET* 3.7 38.8 - - + -
987C VAL* 4.0 10.2 - - + +
991C HIS* 5.8 3.4 - - + +
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Residues in contact with ARG 969 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A LYS 5.7 1.0 + - - -
609A HIS* 5.2 6.7 - - - +
604C ASP* 4.2 9.2 + - - +
605C VAL* 3.1 30.5 - - + +
606C SER 3.8 16.5 + - - -
607C GLU* 5.7 3.4 - - + +
965C ASN* 2.9 29.0 + - - +
966C LYS* 3.7 12.4 - - - +
968C PHE* 1.3 75.6 - - - +
970C ARG* 1.3 67.0 + - - +
972C ARG* 3.3 5.5 + - + +
973C LYS* 2.9 27.2 + - - +
40G T 3.2 6.7 + - - -
41G G 2.5 52.9 + - - -
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Residues in contact with ARG 970 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A GLN* 4.0 14.5 - - - +
475C PHE* 3.7 58.0 - - + -
966C LYS* 2.9 23.6 + - - +
967C LEU* 3.3 10.8 - - - +
969C ARG* 1.3 75.8 - - - +
971C PHE* 1.3 62.7 + - - +
973C LYS* 3.3 2.8 + - - +
974C MET* 3.0 49.1 + - - +
975C ASN* 4.6 0.6 + - - +
21J G 4.0 24.5 + - - -
22J T 4.5 10.5 + - - -
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Residues in contact with PHE 971 (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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472C VAL 4.6 3.6 - - - -
475C PHE* 3.5 32.1 - + - -
967C LEU* 3.0 48.8 + - + +
968C PHE* 3.9 4.3 - - - +
970C ARG* 1.3 80.3 - - - +
972C ARG* 1.3 64.1 + - - +
975C ASN* 3.0 40.6 + - - +
976C ALA* 3.6 5.4 + - - +
987C VAL* 4.1 21.1 - - + +
990C HIS* 3.6 32.3 - + + -
991C HIS* 4.1 21.1 - + + -
994C TYR* 3.9 26.9 - + + -
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Residues in contact with ARG 972 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605C VAL* 3.2 33.8 + - - +
606C SER* 4.4 3.6 - - - +
607C GLU* 4.3 26.2 + - - +
617C GLU* 3.0 36.1 + - - -
659C LEU* 4.0 8.5 - - - +
968C PHE* 3.0 31.3 + - + +
969C ARG* 3.7 5.8 - - - +
971C PHE* 1.3 78.6 - - - +
973C LYS* 1.3 64.9 + - - +
976C ALA* 3.6 17.5 + - - +
978C GLN* 4.2 8.9 - - - +
983C GLU* 3.0 41.8 + - + +
984C MET* 5.9 1.7 - - - -
987C VAL* 3.7 20.3 - - + +
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Residues in contact with LYS 973 (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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607A GLU* 4.8 4.2 + - - -
973A LYS* 3.3 40.4 - - - +
607C GLU* 4.4 25.1 - - + +
969C ARG 2.9 16.5 + - - +
970C ARG* 4.1 2.9 - - - +
972C ARG* 1.3 81.0 - - - +
974C MET* 1.3 70.6 + - + +
976C ALA 4.8 3.5 - - - +
978C GLN* 4.7 6.8 - - - +
22L T 5.2 4.9 - - - +
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Residues in contact with MET 974 (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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970A ARG* 6.3 0.9 - - - +
974A MET* 3.9 31.9 - - + +
474C THR 5.3 0.7 - - - +
475C PHE* 3.4 37.0 - - + +
477C SER* 3.9 10.9 + - - -
970C ARG* 3.0 35.0 + - - +
973C LYS* 1.3 94.1 - - + +
975C ASN* 1.3 68.9 + - - +
976C ALA 3.7 1.3 - - - -
22L T 3.8 19.8 + - - +
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Residues in contact with ASN 975 (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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475C PHE* 3.5 32.0 + - - +
476C LEU 3.2 24.8 - - - +
970C ARG 4.6 0.2 + - - -
971C PHE* 3.0 36.4 + - + +
974C MET* 1.3 83.9 - - - +
976C ALA* 1.3 60.8 + - - +
986C ASP* 4.0 4.7 - - - +
987C VAL* 6.4 0.2 - - - -
990C HIS* 3.5 39.0 + - + +
22L T 3.6 0.9 - - - -
23L G 3.3 29.1 + - - +
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Residues in contact with ALA 976 (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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971C PHE 3.8 6.1 - - - +
972C ARG* 3.6 22.1 + - - +
973C LYS 4.8 2.3 - - - +
974C MET 3.7 0.6 - - - -
975C ASN* 1.3 79.8 - - - +
977C ARG* 1.3 70.1 + - - +
978C GLN* 3.4 6.2 + - - +
983C GLU* 3.9 17.0 - - + +
986C ASP* 3.8 18.4 - - + -
987C VAL* 4.1 7.6 - - + +
22L T 3.7 19.8 + - - +
23L G 4.3 0.2 - - - -
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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