Contacts of the helix formed by residues 803 - 817 (chain D) in PDB entry 4B8L
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 SER 803 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ARG* 5.1 2.2 - - - +
798D ILE* 5.3 3.6 - - - -
799D PRO 3.6 6.0 + - - -
800D ALA* 2.7 27.1 + - - +
802D ALA* 1.3 78.8 - - - +
804D GLY* 1.3 68.4 + - - +
805D ASN* 2.9 2.9 + - - +
806D LEU* 3.4 16.3 + - - +
807D LEU* 3.0 16.5 + - - -
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Residues in contact with GLY 804 (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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97A ARG* 4.5 7.9 - - - +
802D ALA 3.8 3.0 + - - -
803D SER* 1.3 69.6 - - - +
805D ASN* 1.3 52.6 + - - +
807D LEU* 3.0 9.6 + - - +
808D THR* 2.7 42.8 + - - -
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Residues in contact with ASN 805 (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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803D SER* 2.9 5.2 + - - +
804D GLY* 1.3 74.4 - - - +
806D LEU* 1.3 70.2 + - + +
808D THR* 3.1 17.7 + - - -
809D GLN* 3.3 24.5 + - - +
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Residues in contact with LEU 806 (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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800D ALA* 3.3 39.5 - - + +
801D TRP* 4.3 10.2 - - - +
803D SER* 3.4 16.2 - - - +
805D ASN* 1.3 85.2 - - + +
807D LEU* 1.3 58.6 + - - +
809D GLN* 4.1 19.6 - - - +
810D ALA* 3.6 19.4 + - - +
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Residues in contact with LEU 807 (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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97A ARG* 3.5 18.4 - - - +
109A LEU* 4.2 23.1 - - + -
118A ILE* 3.7 25.1 - - + -
172A PHE* 5.0 5.4 - - + -
801D TRP* 3.5 15.7 + - + +
802D ALA* 3.4 20.4 - - - +
803D SER 3.0 19.7 + - - +
804D GLY* 3.2 6.3 - - - +
806D LEU* 1.3 78.2 - - - +
808D THR* 1.3 62.9 + - - +
810D ALA* 3.2 3.4 + - - +
811D ILE* 3.1 40.9 + - + +
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Residues in contact with THR 808 (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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226A TYR* 4.9 10.1 - - + -
804D GLY* 2.7 23.1 + - - -
805D ASN* 3.1 10.6 + - - -
807D LEU* 1.3 75.9 - - - +
809D GLN* 1.3 62.0 + - - +
811D ILE* 3.3 7.9 + - - +
812D ARG* 3.2 50.3 + - + +
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Residues in contact with GLN 809 (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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805D ASN* 3.3 22.1 + - - +
806D LEU* 4.3 20.8 - - - +
807D LEU 3.3 0.2 - - - -
808D THR* 1.3 79.0 - - - +
810D ALA* 1.3 60.0 + - - +
811D ILE 3.4 0.2 - - - -
812D ARG* 3.6 30.8 + - - +
813D GLN* 3.3 30.7 + - - +
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Residues in contact with ALA 810 (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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118A ILE* 3.8 20.0 - - + -
801D TRP 5.4 0.9 - - - +
806D LEU 3.6 14.6 + - - +
807D LEU* 3.2 10.3 + - - +
808D THR 3.2 0.4 - - - -
809D GLN* 1.3 78.7 - - - +
811D ILE* 1.3 63.2 + - - +
813D GLN* 3.6 12.7 + - - +
814D GLN* 3.4 27.3 + - - +
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Residues in contact with ILE 811 (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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118A ILE* 3.9 22.9 - - + -
172A PHE* 3.7 33.7 - - + -
174A PRO* 3.9 21.5 - - + -
226A TYR* 3.8 28.3 - - + -
807D LEU* 3.1 25.3 + - + +
808D THR* 3.3 8.9 + - - +
810D ALA* 1.3 75.1 - - - +
812D ARG* 1.3 65.7 + - - +
813D GLN 3.1 1.8 - - - -
814D GLN* 3.1 10.8 + - + +
815D TYR* 3.0 21.9 + - + +
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Residues in contact with ARG 812 (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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226A TYR* 2.9 35.8 + - + +
808D THR* 3.2 31.8 + - - +
809D GLN* 3.6 37.1 + - - +
811D ILE* 1.3 77.4 - - - +
813D GLN* 1.3 59.3 - - + +
815D TYR* 3.6 2.2 - - - +
816D TYR* 2.9 46.5 + - + +
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Residues in contact with GLN 813 (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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809D GLN* 3.3 20.6 + - - +
810D ALA* 3.8 13.2 - - - +
811D ILE 3.1 0.6 - - - -
812D ARG* 1.3 79.0 - - + +
814D GLN* 1.3 59.6 + - + +
815D TYR 3.1 0.4 - - - -
816D TYR* 5.3 0.9 - - - -
817D LYS* 2.9 39.5 + - + +
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Residues in contact with GLN 814 (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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116A LYS 4.2 2.8 - - - +
117A PHE* 3.3 36.1 - - + -
118A ILE* 2.7 57.0 + - - +
172A PHE* 6.0 1.2 - - - +
810D ALA* 3.4 15.8 - - - +
811D ILE* 3.1 12.8 + - + +
813D GLN* 1.3 76.9 - - + +
815D TYR* 1.3 58.5 + - - +
817D LYS 4.4 3.6 - - - -
818D PRO* 3.4 25.0 - - - +
819D ILE* 4.8 2.2 + - + +
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Residues in contact with TYR 815 (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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226A TYR* 3.4 38.4 - + + -
227A LYS* 3.2 35.3 - - + +
229A GLU* 3.3 32.8 + - - -
350A VAL* 3.9 16.0 + - + +
811D ILE* 3.0 16.2 + - + +
812D ARG 3.6 3.8 - - - +
814D GLN* 1.3 78.5 - - - +
816D TYR* 1.3 86.9 + + - +
818D PRO* 3.6 14.0 - - - +
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Residues in contact with TYR 816 (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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226A TYR* 4.0 21.7 - + - -
227A LYS* 3.8 26.0 + - + +
812D ARG* 2.9 33.7 + - + +
813D GLN* 5.3 0.7 - - - -
815D TYR* 1.3 93.7 - + - +
817D LYS* 1.3 66.6 + - + +
818D PRO* 3.3 7.7 - - - +
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Residues in contact with LYS 817 (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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813D GLN* 2.9 23.4 + - + +
814D GLN* 4.4 0.7 - - - -
816D TYR* 1.3 85.3 - - + +
818D PRO* 1.3 66.4 - - + +
819D ILE* 3.4 6.4 + - - +
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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