Contacts of the helix formed by residues 833 - 843 (chain B) in PDB entry 5KJH
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 833 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832B SER* 1.3 71.9 - - - +
834B ASP* 1.3 69.4 + - - +
836B GLY 3.2 2.1 + - - -
837B VAL* 3.0 34.1 + - + +
864B GLY* 3.2 18.1 + - - +
866B TRP* 4.0 27.6 - + + +
2530B GLU 3.4 25.8 - - - -
2531B VAL* 2.9 30.8 + - + +
2533B LEU* 3.4 28.4 - - + +
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Residues in contact with ASP 834 (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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353B LYS* 4.9 23.1 + - - +
354B SER* 5.7 4.6 - - - -
523B ARG* 5.1 9.0 + - - -
832B SER* 3.6 8.2 + - - +
833B HIS* 1.3 88.9 + - - +
835B GLU* 1.4 60.1 + - - +
837B VAL* 3.3 7.6 + - - +
838B ARG* 3.0 42.7 + - - +
2530B GLU 5.0 1.9 - - - +
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Residues in contact with GLU 835 (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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317B LEU 4.0 6.5 - - - +
318B ASN* 3.4 9.5 - - - +
319B SER* 2.7 49.7 + - - +
831B ILE* 3.9 15.7 - - + -
832B SER* 3.2 24.4 + - - +
834B ASP* 1.4 76.0 - - - +
836B GLY* 1.3 56.7 + - - +
838B ARG* 2.8 31.8 + - - +
839B ARG* 2.9 66.7 + - - +
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Residues in contact with GLY 836 (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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831B ILE* 3.5 21.2 - - - +
832B SER 3.0 10.8 + - - -
833B HIS 3.2 4.9 + - - -
835B GLU* 1.3 73.4 - - - +
837B VAL* 1.3 57.9 + - - +
839B ARG* 3.8 3.1 - - - +
840B GLU* 2.9 35.3 + - - +
856B LEU* 4.7 4.3 - - - -
2533B LEU* 3.7 16.7 - - - +
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Residues in contact with VAL 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.8 27.1 - - + -
353B LYS* 6.1 0.4 - - - +
833B HIS* 3.0 30.9 + - + +
834B ASP* 3.3 9.8 + - - +
836B GLY* 1.3 73.3 - - - +
838B ARG* 1.4 65.7 + - - +
841B HIS* 3.1 44.7 + - + +
2530B GLU* 3.2 35.9 - - - +
2532B MET 4.9 3.1 - - - +
2533B LEU* 3.8 17.9 - - + +
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Residues in contact with ARG 838 (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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318B ASN* 3.0 32.7 + - - +
319B SER 2.8 42.7 + - - +
350B LEU* 4.3 25.1 - - + +
351B ASP* 4.0 18.6 - - - +
354B SER* 4.2 28.0 + - - +
356B PHE* 6.3 0.4 - - - -
832B SER* 4.3 0.4 + - - -
834B ASP* 3.0 26.0 + - - +
835B GLU* 2.8 37.3 + - - +
837B VAL* 1.4 75.6 - - - +
839B ARG* 1.4 56.3 + - - +
841B HIS* 3.4 1.6 + - - +
842B ARG* 3.0 47.4 + - + +
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Residues in contact with ARG 839 (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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184A GLU* 4.9 4.9 + - - -
316B ALA* 3.9 13.1 - - - +
317B LEU 4.7 2.8 + - - -
319B SER* 6.0 0.8 - - - -
829B GLU* 2.9 44.7 + - - -
831B ILE* 3.8 15.2 - - - +
835B GLU* 2.9 50.7 + - - +
836B GLY* 3.8 4.0 - - - +
838B ARG* 1.4 71.8 - - - +
840B GLU* 1.3 63.3 + - - +
841B HIS 3.3 0.3 + - - -
842B ARG* 3.3 24.4 + - - +
843B ARG* 3.1 55.5 + - - +
856B LEU* 6.2 0.4 - - + -
868B ASP* 2.8 40.0 + - - +
871B ILE* 6.1 0.2 - - - +
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Residues in contact with GLU 840 (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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836B GLY 2.9 19.6 + - - +
837B VAL 4.0 2.9 - - - +
839B ARG* 1.3 73.9 - - - +
841B HIS* 1.3 65.3 + - + +
843B ARG* 3.7 20.9 + - - +
844B GLY* 3.2 22.5 + - - -
853B VAL 4.0 5.7 - - - +
854B SER* 3.3 29.8 - - - -
855B TYR 5.4 0.5 + - - -
856B LEU* 3.5 33.5 - - + +
868B ASP* 5.3 0.2 - - - +
2533B LEU* 4.3 10.3 - - + -
2534B PRO* 4.9 11.9 - - + -
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Residues in contact with HIS 841 (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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343B TRP* 3.2 30.4 + + - +
346B ASP* 5.7 5.5 - - - +
347B LEU* 3.5 18.2 - - + +
350B LEU* 3.5 20.9 - - + +
837B VAL* 3.1 40.4 + - + +
838B ARG 3.9 2.5 - - - +
840B GLU* 1.3 80.5 - - + +
842B ARG* 1.4 64.4 + - - +
844B GLY* 3.3 6.0 + - - -
2530B GLU* 4.7 14.1 + - - -
2532B MET 5.2 7.1 + - - -
2533B LEU* 6.0 1.1 - - + +
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Residues in contact with ARG 842 (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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187A SER* 6.3 0.4 - - - -
188A TYR* 4.1 17.5 - - - -
319B SER* 2.8 44.4 + - - -
320B GLN 4.1 7.4 + - - -
321B LEU* 3.7 45.3 - - + +
323B PHE* 5.6 7.3 - - + -
325B PRO* 4.4 4.0 - - - +
343B TRP* 4.1 11.9 - - - -
347B LEU* 4.2 12.1 - - + -
351B ASP* 5.8 0.8 + - - -
835B GLU* 4.5 0.6 + - - -
838B ARG* 3.0 34.9 + - + +
839B ARG* 3.6 28.3 - - - +
841B HIS* 1.4 75.5 - - - +
843B ARG* 1.3 68.8 + - + +
844B GLY 3.2 1.7 + - - +
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Residues in contact with ARG 843 (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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188A TYR* 5.5 5.2 - - - -
304B ARG* 5.4 13.0 - - - +
305B PHE* 4.2 27.7 - - + -
839B ARG* 3.1 52.2 + - - +
840B GLU* 3.8 18.4 + - - +
842B ARG* 1.3 81.8 - - + +
844B GLY* 1.3 63.5 + - - +
845B ASP* 5.3 0.3 - - - +
868B ASP* 2.9 30.8 + - - -
870B ALA* 3.3 25.4 - - - +
871B ILE* 4.9 8.7 - - - +
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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