Contacts of the helix formed by residues 797 - 807 (chain B) in PDB entry 1HKB
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 LEU 797 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B GLU* 3.2 48.1 + - + +
796B ALA* 1.3 71.5 - - - +
798B LEU* 1.3 62.8 + - - +
800B VAL* 3.1 14.1 + - + +
801B ARG* 2.9 24.3 + - - +
813B CYS* 4.1 25.5 - - + +
816B SER* 4.2 15.5 - - - -
817B ILE* 3.3 47.1 - - + +
820B LYS* 5.4 7.0 - - + -
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Residues in contact with LEU 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.4 42.8 - - + +
55A PHE* 3.7 27.8 - - + -
249B GLU* 4.5 2.2 + - - -
251B ASP* 5.4 3.4 - - - +
796B ALA* 3.0 4.4 + - + +
797B LEU* 1.3 77.9 - - - +
799B GLN* 1.3 67.9 + - - +
801B ARG* 3.5 23.1 + - - +
802B ALA* 3.1 20.3 + - - +
813B CYS* 5.1 7.6 - - - -
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Residues in contact with GLN 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP 3.6 25.8 + - - +
55A PHE* 3.6 20.5 + - - +
57A PRO* 3.9 2.6 - - - +
58A THR* 2.9 47.7 + - - +
795B LEU* 3.2 30.7 - - + +
796B ALA* 2.6 21.2 + - - +
798B LEU* 1.3 76.1 - - + +
800B VAL* 1.3 63.8 + - - +
802B ALA* 2.9 13.0 + - - +
803B ILE* 2.9 27.8 + - + +
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Residues in contact with VAL 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790B ILE* 4.2 28.7 - - + +
795B LEU* 3.8 23.6 - - + -
796B ALA 3.0 15.6 + - - +
797B LEU* 3.5 18.4 - - + +
799B GLN* 1.3 77.6 - - - +
801B ARG* 1.3 64.9 + - - +
803B ILE* 3.2 7.4 + - - +
804B LEU* 3.1 23.8 + - + +
816B SER* 3.8 26.9 - - - +
820B LYS* 4.1 22.9 - - + +
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Residues in contact with ARG 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ASP* 2.9 36.8 + - - -
252B GLU* 3.2 15.1 + - - -
797B LEU 2.9 11.2 + - - +
798B LEU* 3.7 24.2 + - - +
800B VAL* 1.3 77.2 - - - +
802B ALA* 1.3 64.1 + - - +
804B LEU* 3.5 5.3 + - - +
805B GLN* 3.1 35.5 + - - +
811B SER* 3.2 28.9 + - - +
812B THR* 3.9 8.7 - - - +
813B CYS* 3.1 28.7 - - - -
816B SER* 3.3 19.5 + - - +
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Residues in contact with ALA 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 4.7 11.7 - - + -
798B LEU 3.1 13.2 + - - +
799B GLN* 2.9 23.8 + - - +
801B ARG* 1.3 75.7 - - - +
803B ILE* 1.3 65.2 + - - +
805B GLN* 2.9 24.3 + - - +
806B GLN* 3.0 18.4 + - + +
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Residues in contact with ILE 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 4.4 14.1 - - + +
786B PHE* 4.9 16.6 - - + +
789B GLN* 4.1 32.5 - - + +
790B ILE* 4.6 9.6 - - + +
795B LEU* 3.8 29.4 - - + -
799B GLN* 2.9 23.9 + - + +
800B VAL* 3.6 8.3 - - - +
802B ALA* 1.3 74.8 - - - +
804B LEU* 1.3 65.6 + - + +
806B GLN* 3.1 32.1 + - - +
807B LEU* 3.1 18.9 + - + +
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Residues in contact with LEU 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768B PHE* 5.3 0.4 - - + -
782B PHE* 4.5 9.2 - - + -
790B ILE* 4.9 6.1 - - + -
800B VAL* 3.1 16.4 + - + +
801B ARG 3.7 6.1 - - - +
803B ILE* 1.3 81.0 - - + +
805B GLN* 1.3 60.0 + - - +
807B LEU* 2.9 27.4 + - + +
809B LEU* 3.1 43.6 + - + +
811B SER* 3.5 24.5 - - - +
816B SER* 4.0 29.2 - - - +
819B VAL* 4.1 33.4 - - + -
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Residues in contact with GLN 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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801B ARG* 3.1 31.1 + - - +
802B ALA* 2.9 12.1 + - - +
804B LEU* 1.3 79.7 - - - +
806B GLN* 1.3 63.7 + - - +
808B GLY* 2.9 14.6 + - - -
809B LEU 3.1 18.7 + - - +
810B ASN* 4.3 11.8 + - - +
811B SER 3.1 24.4 + - - +
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Residues in contact with GLN 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 6.0 2.8 - - - +
786B PHE* 6.2 1.6 - - - -
802B ALA* 3.0 15.2 + - + +
803B ILE* 3.2 28.9 + - - +
805B GLN* 1.3 77.8 - - - +
807B LEU* 1.3 61.6 - - + +
808B GLY* 3.2 1.6 + - - -
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Residues in contact with LEU 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775B THR* 2.9 25.6 + - + +
781B ILE* 4.3 32.3 - - + +
782B PHE* 4.0 31.9 - - + -
786B PHE* 4.3 33.0 - - + -
803B ILE* 3.1 19.5 + - + +
804B LEU* 2.9 19.6 + - + +
806B GLN* 1.3 76.6 - - + +
808B GLY* 1.3 57.4 + - - +
809B LEU* 4.4 11.2 - - + -
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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