Contacts of the helix formed by residues 74 - 92 (chain 6) in PDB entry 6CP3
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 74 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726 SER 3.7 7.4 - - - +
736 GLU* 1.3 88.7 - - + +
756 ILE* 1.3 66.9 + - + +
766 GLU 3.7 0.9 - - - -
776 GLU* 3.3 3.1 + - - +
786 ASP* 2.5 56.8 + - - +
917 VAL* 5.2 2.7 - - + -
947 SER* 3.4 31.0 - - - +
957 PHE* 4.2 14.1 - - + -
987 HIS* 4.3 9.0 - - - +
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Residues in contact with ILE 75 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736 GLU* 3.4 3.4 + - - +
746 PRO* 1.3 87.9 - - + +
766 GLU* 1.3 68.7 + - + +
776 GLU 2.9 6.2 + - - -
786 ASP* 3.1 2.9 + - - +
796 TRP* 3.0 53.3 + - + +
987 HIS* 5.4 9.2 - - + +
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Residues in contact with GLU 76 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736 GLU* 2.7 21.2 + - - +
756 ILE* 1.3 83.7 - - + +
776 GLU* 1.3 60.1 + - + +
796 TRP* 4.7 4.5 - - - -
806 LEU* 3.4 25.2 - - - +
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Residues in contact with GLU 77 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736 GLU* 3.2 28.8 + - - +
746 PRO 3.3 2.2 + - - +
756 ILE 3.0 0.4 - - - -
766 GLU* 1.3 82.9 - - + +
786 ASP* 1.3 61.2 + - - +
796 TRP 3.3 1.1 - - - -
806 LEU* 3.7 12.2 - - + +
816 VAL* 2.9 35.4 + - + +
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Residues in contact with ASP 78 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746 PRO* 2.5 40.2 + - + +
756 ILE* 4.1 2.5 - - - +
776 GLU* 1.3 69.6 - - - +
796 TRP* 1.3 63.6 + - + +
816 VAL* 3.4 13.1 + - - +
826 LEU* 2.9 29.5 + - - +
957 PHE* 3.2 38.1 - - - -
987 HIS* 3.9 23.1 - - + +
5U ILE* 5.8 2.3 - - - +
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Residues in contact with TRP 79 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756 ILE* 3.0 53.0 + - + +
766 GLU* 5.0 3.6 - - - -
786 ASP* 1.3 78.1 - - + +
806 LEU* 1.3 60.3 + - + +
826 LEU* 3.3 30.1 + - + +
836 ASP* 2.9 43.3 + - - +
987 HIS* 5.8 11.0 - + - -
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Residues in contact with LEU 80 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766 GLU 3.4 22.4 - - - +
776 GLU* 3.3 15.7 + - + +
786 ASP 3.3 0.4 - - - -
796 TRP* 1.3 78.6 - - + +
816 VAL* 1.3 59.0 + - + +
836 ASP* 3.4 8.8 + - + +
846 ASP* 2.9 46.4 + - - +
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Residues in contact with VAL 81 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776 GLU* 2.9 23.4 + - + +
786 ASP* 3.7 13.7 - - - +
796 TRP 3.4 0.2 - - - -
806 LEU* 1.3 76.3 - - + +
826 LEU* 1.3 57.9 + - - +
846 ASP* 3.8 4.6 - - - +
856 ALA* 2.8 32.4 + - + +
4U LEU* 4.2 24.2 - - + -
5U ILE* 3.7 30.5 - - + +
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Residues in contact with LEU 82 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786 ASP 2.9 18.1 + - - +
796 TRP* 3.6 37.0 - - + +
806 LEU 3.2 0.2 - - - -
816 VAL* 1.3 77.0 - - - +
836 ASP* 1.3 62.2 + - - +
856 ALA* 3.3 5.6 + - - +
866 GLU* 3.0 26.4 + - + +
1027 ASN* 4.0 33.2 - - - +
5U ILE* 5.7 6.1 - - + +
9U VAL* 3.6 34.1 - - + +
11U SER* 5.8 2.7 - - - +
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Residues in contact with ASP 83 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796 TRP* 2.9 29.1 + - - +
806 LEU* 4.1 8.6 - - + +
826 LEU* 1.3 80.1 - - - +
846 ASP* 1.3 64.0 + - - +
866 GLU* 3.2 14.2 + - - +
876 GLU* 3.0 30.2 + - - +
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Residues in contact with ASP 84 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806 LEU* 2.9 33.2 + - - +
816 VAL* 4.1 4.4 - - - +
836 ASP* 1.3 79.4 - - - +
856 ALA* 1.3 57.3 + - - +
876 GLU* 3.1 23.6 + - - +
886 THR* 2.9 33.1 + - + +
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Residues in contact with ALA 85 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816 VAL* 2.8 19.5 + - + +
826 LEU* 3.5 6.5 - - - +
836 ASP 3.2 0.2 - - - -
846 ASP* 1.3 74.9 - - - +
866 GLU* 1.3 59.3 + - - +
886 THR* 2.5 24.8 + - - -
896 LYS* 2.9 17.7 + - - +
4U LEU* 6.4 0.9 - - + -
5U ILE 3.7 23.8 - - - +
6U PRO* 4.1 10.6 - - + +
9U VAL* 3.7 14.9 - - + +
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Residues in contact with GLU 86 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826 LEU* 3.0 19.4 + - + +
836 ASP* 3.3 17.5 - - - +
856 ALA* 1.3 75.8 - - - +
876 GLU* 1.3 58.0 + - + +
896 LYS* 3.3 3.4 + - - +
906 GLU* 2.9 37.6 + - + +
9U VAL* 2.8 34.2 - - + +
11U SER* 4.6 0.2 + - - -
12U SER* 2.7 44.5 + - - +
13U LYS* 3.1 19.1 + - - +
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Residues in contact with GLU 87 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 ASP* 3.0 15.7 + - - +
846 ASP* 3.1 28.4 + - - +
866 GLU* 1.3 73.5 - - + +
886 THR* 1.3 60.7 + - + +
906 GLU* 3.3 23.6 - - - +
916 SER* 3.0 25.8 + - - -
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Residues in contact with THR 88 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846 ASP* 2.9 21.0 + - + +
856 ALA* 2.5 27.3 + - - -
876 GLU* 1.3 75.5 - - + +
896 LYS* 1.3 50.6 + - - +
916 SER* 2.6 13.3 + - - +
926 HIS* 2.4 58.0 + - - -
237 GLY 4.7 3.6 - - - +
257 THR* 3.6 25.1 - - - +
4U LEU* 6.4 0.7 - - + -
6U PRO* 3.9 11.1 - - + +
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Residues in contact with LYS 89 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856 ALA 2.9 13.4 + - - +
866 GLU* 3.9 5.4 - - - +
886 THR* 1.3 76.9 + - - +
906 GLU* 1.3 60.7 + - - +
926 HIS* 3.0 35.7 - - + +
217 ILE* 4.0 20.9 - - + +
6U PRO* 5.9 4.7 - - + +
7U PRO 5.9 1.7 + - - -
9U VAL* 3.8 19.3 - - + +
10U VAL* 3.6 29.2 - - + +
13U LYS* 3.7 48.6 - - + +
113Z LEU* 4.3 14.2 - - - +
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Residues in contact with GLU 90 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866 GLU* 2.9 24.7 + - - +
876 GLU* 3.3 25.5 - - - +
896 LYS* 1.3 78.8 - - - +
916 SER* 1.3 61.2 + - - +
926 HIS 3.5 4.2 + - - +
13U LYS* 5.4 2.8 - - + +
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Residues in contact with SER 91 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876 GLU 3.0 9.9 + - - -
886 THR* 2.6 30.2 + - - +
906 GLU* 1.3 73.1 - - - +
926 HIS* 1.3 66.7 + - - +
227 THR* 4.4 6.3 + - - +
237 GLY* 5.3 2.9 + - - -
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Residues in contact with HIS 92 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886 THR* 2.4 58.6 + - - +
896 LYS* 3.0 29.6 - - + +
906 GLU 3.3 4.4 - - - +
916 SER* 1.3 75.1 - - - +
207 ARG 5.2 2.0 - - - +
217 ILE* 3.1 56.2 - - + +
227 THR* 2.5 44.4 + - - -
237 GLY 3.4 19.2 + - - -
247 SER* 3.8 3.8 - - - -
6U PRO* 4.8 9.1 - - + +
13U LYS* 5.9 0.5 - - - -
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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