Contacts of the helix formed by residues 982 - 995 (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 TYR 982 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977C ARG* 3.5 55.0 - - + +
979C SER* 3.1 18.3 + - - +
981C CYS* 1.3 106.1 - - + +
983C GLU* 1.3 67.9 + - - +
984C MET 3.3 2.5 - - - -
985C GLU* 3.1 22.3 + - - +
986C ASP* 3.0 24.5 + - - -
26F C 4.8 14.2 + - - -
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Residues in contact with GLU 983 (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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553C ILE* 3.3 22.6 - - - +
659C LEU* 4.1 3.4 - - - +
972C ARG* 3.0 46.1 + - + +
976C ALA* 4.2 9.4 - - + -
977C ARG 3.4 21.7 + - - +
978C GLN* 4.2 13.2 + - - +
979C SER 2.9 17.9 + - - +
980C LYS* 3.9 18.5 - - - +
982C TYR* 1.3 77.5 - - - +
984C MET* 1.3 70.3 + - + +
986C ASP* 3.2 2.1 + - - +
987C VAL* 2.9 34.5 + - - +
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Residues in contact with MET 984 (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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553C ILE* 4.2 34.8 - - + +
554C ALA 4.8 0.2 - - - -
555C LYS* 3.6 24.2 - - + +
657C LEU* 3.4 47.1 - - + +
658C MET* 3.9 9.9 - - - +
659C LEU* 4.4 10.1 - - + -
968C PHE* 3.7 29.4 - - + -
972C ARG* 5.9 1.8 - - - -
980C LYS 4.9 2.6 + - - +
981C CYS 5.9 0.2 - - - +
982C TYR 3.3 0.4 - - - -
983C GLU* 1.3 79.2 - - + +
985C GLU* 1.3 69.0 + - - +
987C VAL* 3.7 5.7 - - - +
988C LEU* 2.9 26.9 + - - +
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Residues in contact with GLU 985 (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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534C ILE* 3.5 39.0 - - + +
555C LYS* 3.8 21.5 + - + +
977C ARG* 4.5 8.4 + - - -
981C CYS 4.4 6.2 - - - +
982C TYR* 3.1 33.4 + - + +
984C MET* 1.3 79.4 - - - +
986C ASP* 1.3 62.5 + - - +
988C LEU* 3.7 0.2 - - - +
989C LYS* 3.0 31.3 + - + +
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Residues in contact with ASP 986 (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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975C ASN 4.0 4.9 - - - +
976C ALA* 3.8 21.3 - - + -
977C ARG* 2.8 57.3 + - - -
982C TYR 3.0 15.3 + - - +
985C GLU* 1.3 75.3 - - - +
987C VAL* 1.3 66.5 + - - +
989C LYS* 3.6 12.0 + - - +
990C HIS* 2.9 31.1 + - - +
23L G 3.5 18.9 - - - +
24L A 4.5 2.8 + - - -
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Residues in contact with VAL 987 (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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657C LEU* 3.7 21.1 - - + -
968C PHE* 4.0 22.0 - - + +
971C PHE* 4.1 16.3 - - + +
972C ARG* 3.7 39.3 - - + +
976C ALA* 4.1 6.1 - - + -
983C GLU 2.9 24.1 + - - +
984C MET* 3.7 10.1 - - - +
986C ASP* 1.3 75.4 - - - +
988C LEU* 1.3 63.8 + - - +
990C HIS* 3.2 5.6 + - - +
991C HIS* 2.9 23.7 + - + +
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Residues in contact with LEU 988 (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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534C ILE* 4.1 8.1 - - + -
555C LYS* 3.8 35.2 - - + +
556C ARG* 3.9 11.4 - - - +
557C PHE* 3.8 35.2 - - + -
654C PRO* 4.1 20.9 - - + +
655C LEU 4.6 4.7 - - - -
657C LEU* 4.1 30.5 - - + +
984C MET 2.9 16.1 + - - +
985C GLU 3.7 1.6 - - - +
987C VAL* 1.3 78.2 - - - +
989C LYS* 1.3 63.8 + - - +
990C HIS 3.1 0.2 + - - -
991C HIS* 3.2 3.6 + - - +
992C TRP* 2.9 23.2 + - - +
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Residues in contact with LYS 989 (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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471C ARG* 5.6 0.2 - - - +
507C GLU* 3.0 41.1 + - - -
511C LEU* 3.6 37.0 - - + +
534C ILE* 3.9 16.7 - - + +
557C PHE* 4.9 0.9 - - - -
985C GLU* 3.0 17.3 + - + +
986C ASP* 3.9 11.1 + - - +
988C LEU* 1.3 76.5 - - - +
990C HIS* 1.3 74.1 + - - +
992C TRP* 3.4 3.5 + - - +
993C LEU* 3.0 36.5 + - + +
23L G 5.3 4.4 + - - -
24L A 4.1 19.1 + - - +
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Residues in contact with HIS 990 (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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471C ARG* 3.8 26.2 + - - -
472C VAL* 4.1 28.6 - - + +
476C LEU 5.0 1.2 + - - -
507C GLU* 5.4 0.4 - - - -
971C PHE* 3.6 35.6 - + + +
975C ASN* 3.5 40.2 + - + -
986C ASP* 2.9 23.3 + - - +
987C VAL* 3.6 4.9 - - - +
989C LYS* 1.3 89.0 + - - +
991C HIS* 1.3 60.4 + - - +
993C LEU* 3.4 7.5 + - + +
994C TYR* 2.9 28.0 + - - +
23L G 4.5 5.8 - - - -
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Residues in contact with HIS 991 (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* 6.3 1.3 - - - -
621C ARG* 4.6 19.1 - - + -
649C GLU* 4.7 5.9 + - - +
652C CYS* 4.3 7.7 + - - +
654C PRO* 3.8 22.2 - - + +
657C LEU* 4.5 12.5 - - + +
964C GLY* 5.9 4.0 - - - -
967C LEU* 3.4 35.3 - - + +
968C PHE* 5.8 4.3 - - + -
971C PHE* 4.1 9.0 - - + -
987C VAL* 2.9 17.1 + - + +
988C LEU* 3.6 5.6 - - - +
990C HIS* 1.3 73.8 - - - +
992C TRP* 1.3 66.1 + - - +
994C TYR* 2.9 18.7 + + - +
995C THR* 3.0 37.9 + - + +
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Residues in contact with TRP 992 (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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510C LEU 2.9 29.0 + - - -
511C LEU* 3.8 15.5 - - + -
512C PRO* 3.5 10.9 - - + +
557C PHE* 3.5 21.3 - + + -
562C ALA* 3.6 33.7 - - + -
565C SER* 3.7 23.1 + - - -
566C ALA* 4.1 4.3 - - + -
624C PHE* 4.2 4.3 - + - -
653C LYS* 3.3 41.4 - - + +
654C PRO* 3.3 41.6 - - + +
988C LEU 2.9 16.7 + - - +
989C LYS 3.7 4.0 - - - +
991C HIS* 1.3 75.3 - - - +
993C LEU* 1.3 67.4 + - - +
995C THR* 2.8 20.6 + - - -
996C SER* 3.5 8.2 + - - -
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Residues in contact with LEU 993 (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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468C LEU* 4.0 14.6 - - + -
472C VAL* 4.2 24.1 - - + +
507C GLU* 3.6 35.2 - - + +
510C LEU* 3.6 34.1 - - + +
511C LEU* 4.2 11.4 - - + -
989C LYS* 3.0 35.8 + - + +
990C HIS* 3.7 7.2 - - + +
992C TRP* 1.3 77.3 - - - +
994C TYR* 1.3 62.2 + - - +
995C THR 3.1 1.4 + - - -
996C SER* 3.3 11.0 + - - +
999C LEU* 3.5 22.4 - - + +
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Residues in contact with TYR 994 (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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483A LYS* 6.3 0.2 - - - -
472C VAL* 4.0 12.7 - - + +
473C ASN* 3.7 34.8 + - - +
475C PHE* 4.4 18.4 - + - -
649C GLU* 4.8 11.8 - - + +
650C LEU* 4.3 23.7 - - + +
967C LEU* 3.3 34.3 - - + +
971C PHE* 3.9 18.4 - + + -
990C HIS 2.9 14.6 + - - +
991C HIS* 2.9 19.5 + + - +
993C LEU* 1.3 78.0 - - - +
995C THR* 1.3 60.5 + - + +
996C SER 3.5 0.4 + - - -
1000C GLN* 3.6 15.2 + - - +
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Residues in contact with THR 995 (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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649C GLU 4.2 7.4 - - - +
650C LEU 3.2 26.1 - - - +
651C CYS* 4.6 2.1 - - - -
652C CYS 3.9 8.3 - - - +
653C LYS* 3.2 37.8 + - - +
654C PRO* 3.8 14.3 - - + +
991C HIS* 3.1 33.2 - - + +
992C TRP 2.8 17.7 + - - -
994C TYR* 1.3 80.9 - - + +
996C SER* 1.3 61.3 + - - +
997C LYS* 3.5 2.9 + - - +
1000C GLN* 3.3 5.5 + - - -
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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