Contacts of the helix formed by residues 865 - 875 (chain D) in PDB entry 6PB4
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 HIS 865 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840D LEU* 4.5 7.6 - - - -
841D GLY* 5.0 0.4 - - - +
863D LEU* 2.9 38.7 + - + +
864D LEU* 1.3 80.2 - - - +
866D GLU* 1.3 56.1 + - - +
867D GLN* 2.4 41.0 + - + +
868D TRP* 2.8 53.3 + + - +
869D CYS* 3.1 7.6 + - - -
901D ARG* 4.8 16.4 - - - +
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Residues in contact with GLU 866 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836D ARG* 2.6 35.1 + - - +
840D LEU* 2.9 32.9 - - + +
865D HIS* 1.3 73.6 + - - +
867D GLN* 1.3 66.0 + - - +
868D TRP 3.3 0.2 - - - -
869D CYS* 3.1 14.2 - - - +
870D ASP* 2.6 63.7 + - - +
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Residues in contact with GLN 867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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865D HIS* 2.4 44.2 + - + +
866D GLU* 1.3 83.0 + - - +
868D TRP* 1.3 59.9 + - + +
870D ASP* 3.3 9.2 + - - +
871D LEU* 2.9 33.7 + - + +
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Residues in contact with TRP 868 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857D LEU* 3.8 46.9 - - + -
862D THR* 4.8 13.0 + - + -
863D LEU 3.2 24.1 + - - -
864D LEU* 4.1 14.6 - - + -
865D HIS* 2.8 51.0 + + - +
867D GLN* 1.3 77.6 - - + +
869D CYS* 1.3 56.6 + - - +
871D LEU* 3.4 31.9 - - + +
872D LEU* 2.9 28.4 + - - +
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Residues in contact with CYS 869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836D ARG* 4.0 22.2 - - + +
839D VAL* 4.7 8.5 - - - -
840D LEU* 3.6 30.7 - - - -
864D LEU 3.5 24.7 - - - -
865D HIS 3.1 4.8 + - - -
866D GLU* 3.1 22.9 - - - +
867D GLN 3.2 0.4 - - - -
868D TRP* 1.3 78.8 - - - +
870D ASP* 1.3 56.5 + - - +
872D LEU* 3.3 8.3 - - - +
873D GLU* 2.8 28.8 + - - +
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Residues in contact with ASP 870 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836D ARG* 4.2 4.9 + - - -
866D GLU* 2.6 50.1 + - - +
867D GLN* 3.7 7.8 + - - +
869D CYS* 1.3 73.6 - - - +
871D LEU* 1.3 59.2 + - - +
872D LEU 3.0 1.3 - - - -
873D GLU* 2.8 27.8 + - - +
874D GLU* 3.0 14.2 + - - +
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Residues in contact with LEU 871 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850D LYS* 3.5 34.3 - - - +
857D LEU* 4.2 11.4 - - + -
867D GLN* 2.9 19.4 + - + +
868D TRP* 3.4 35.4 - - + +
870D ASP* 1.3 75.7 - - - +
872D LEU* 1.3 54.9 + - - +
874D GLU* 3.4 14.7 - - - +
875D ASN* 2.7 24.3 - - - +
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Residues in contact with LEU 872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835D LEU* 5.4 11.0 - - + -
836D ARG* 5.3 15.0 - - + +
839D VAL* 5.3 16.2 - - + -
868D TRP 2.9 13.8 + - - +
869D CYS* 3.3 12.3 - - - +
870D ASP 3.0 0.2 - - - -
871D LEU* 1.3 75.4 - - - +
873D GLU* 1.3 65.7 + - + +
874D GLU 3.0 2.5 - - - -
875D ASN* 2.2 50.1 + - - +
877D VAL* 3.3 38.8 - - + +
880D VAL* 5.7 6.1 - - + -
990D ARG* 5.0 4.9 - - - +
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Residues in contact with GLU 873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836D ARG* 3.1 36.5 + - + -
869D CYS 2.8 14.9 + - - +
870D ASP* 2.8 17.6 + - - +
872D LEU* 1.3 81.6 - - + +
874D GLU* 1.3 62.6 + - - +
875D ASN 3.9 0.7 - - - -
990D ARG* 3.1 26.5 + - - +
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Residues in contact with GLU 874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850D LYS* 5.5 0.3 - - - +
870D ASP 3.0 10.5 + - - +
871D LEU* 3.4 13.5 - - - +
873D GLU* 1.3 77.4 - - - +
875D ASN* 1.3 95.9 + - - +
876D SER* 3.6 2.4 + - - -
990D ARG* 3.5 3.8 + - - -
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Residues in contact with ASN 875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850D LYS* 4.0 26.4 - - - +
851D PRO* 3.6 33.2 - - + +
852D GLY 5.2 0.6 - - - +
871D LEU* 2.7 24.1 - - - +
872D LEU* 2.2 31.9 + - - +
874D GLU* 1.3 101.1 + - - +
876D SER* 1.3 54.1 + - - +
877D VAL* 3.1 17.6 + - + +
990D ARG* 2.2 26.9 + - - -
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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