Contacts of the helix formed by residues 981 - 990 (chain C) in PDB entry 3CMM
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 PRO 981 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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936C ASP* 3.3 30.7 - - - +
937C ILE 3.3 8.7 - - - +
938C LYS* 3.8 10.7 - - + +
979C ASN 3.7 7.2 - - - +
980C LEU* 1.4 87.6 - - + +
982C ILE* 1.3 60.9 + - - +
983C THR* 3.2 0.9 - - - -
984C GLN* 2.9 35.6 + - + +
985C LEU* 2.8 24.1 + - - +
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Residues in contact with ILE 982 (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 ASP* 3.8 7.4 + - + +
937C ILE* 3.1 40.8 + - + +
939C LEU* 5.2 6.1 - - + +
942C LEU* 3.8 10.1 - - + -
957C LEU* 6.0 1.6 - - + -
964C LEU* 4.5 10.8 - - + -
981C PRO* 1.3 68.8 - - - +
983C THR* 1.3 61.8 + - - +
985C LEU* 3.5 12.0 - - + +
986C VAL* 2.9 29.9 + - + +
1001C MET* 4.3 14.6 - - - -
1003C LEU* 4.0 30.3 - - + -
1022C ILE* 3.6 34.1 - - + -
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Residues in contact with THR 983 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936C ASP* 2.9 29.3 + - - +
981C PRO* 5.2 1.3 - - - -
982C ILE* 1.3 79.5 - - - +
984C GLN* 1.3 62.6 + - + +
986C VAL* 3.3 7.9 + - - +
987C LYS* 2.9 25.8 + - + +
994C ILE* 3.7 43.1 - - + +
1001C MET* 5.0 10.4 - - + +
1024C LEU* 3.9 13.3 - - - +
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Residues in contact with GLN 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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980C LEU* 4.2 23.0 - - + +
981C PRO* 2.9 37.6 + - + +
983C THR* 1.3 81.1 - - + +
985C LEU* 1.3 61.1 + - - +
987C LYS* 3.6 13.7 - - + +
988C LEU* 2.8 31.2 + - - +
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Residues in contact with LEU 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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939C LEU* 4.1 33.7 - - + -
957C LEU* 4.9 2.9 - - + -
964C LEU* 3.7 44.0 - - + +
977C ARG* 3.7 37.7 - - + +
980C LEU* 4.2 11.3 - - + +
981C PRO 2.8 13.4 + - - +
982C ILE* 3.5 17.0 - - + +
984C GLN* 1.3 77.7 - - - +
986C VAL* 1.3 60.8 + - - +
988C LEU* 3.4 3.5 + - + +
989C VAL* 3.1 34.2 + - + +
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Residues in contact with VAL 986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959C TYR* 3.6 41.5 - - + -
964C LEU* 3.9 25.8 - - + -
982C ILE* 2.9 22.1 + - + +
983C THR* 3.4 10.8 - - - +
985C LEU* 1.3 76.3 - - - +
987C LYS* 1.3 59.3 + - - +
990C THR* 2.9 49.4 + - + +
993C ASP* 4.3 13.7 - - + +
994C ILE* 4.7 5.6 - - + +
1001C MET* 4.8 9.6 - - + -
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Residues in contact with LYS 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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983C THR* 2.9 17.6 + - + +
984C GLN* 3.3 16.1 + - + +
986C VAL* 1.3 78.6 - - - +
988C LEU* 1.3 59.6 + - - +
991C LYS 3.1 29.4 - - - +
992C LYS* 4.8 14.7 - - - +
993C ASP* 3.3 43.0 + - - +
994C ILE* 4.0 15.2 - - + +
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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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976C GLU* 3.6 31.2 - - + +
977C ARG* 4.2 23.6 - - + +
980C LEU* 4.0 23.1 - - + -
984C GLN 2.8 17.4 + - - +
985C LEU* 3.6 9.0 - - + +
986C VAL 3.2 0.2 - - - -
987C LYS* 1.3 80.3 - - - +
989C VAL* 1.3 64.4 + - + +
991C LYS* 3.7 9.5 + - - +
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Residues in contact with VAL 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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962C SER* 3.9 20.2 - - - -
963C LEU 3.4 21.3 - - - +
964C LEU* 3.9 14.4 - - + -
977C ARG* 3.5 36.3 - - - +
985C LEU* 3.1 22.0 + - + +
986C VAL 4.1 0.4 - - - +
988C LEU* 1.3 76.6 - - + +
990C THR* 1.3 55.1 + - - +
991C LYS* 2.7 20.5 + - - +
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Residues in contact with THR 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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959C TYR* 5.1 6.3 - - + -
962C SER* 3.3 28.3 - - - +
964C LEU* 5.6 0.7 - - + -
986C VAL* 2.9 37.6 + - + +
989C VAL* 1.3 67.7 - - + +
991C LYS* 1.3 54.0 + - - +
992C LYS* 2.5 23.0 + - - +
993C ASP* 3.3 28.8 + - + +
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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