Contacts of the helix formed by residues 697 - 702 (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 CYS 697 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685B CYS* 3.9 6.5 - - - -
687B HIS* 3.4 33.2 - - + +
690B PRO 4.4 0.4 - - - +
691B CYS* 3.5 32.1 - - - -
692B THR 3.1 15.8 + - - +
695B ASN 3.3 2.2 - - - -
696B GLY* 1.4 75.1 - - - +
698B PRO* 1.4 60.6 - - - +
699B CYS* 3.6 22.4 - - - -
700B ALA* 3.3 9.1 + - + +
701B SER* 2.7 34.4 + - - -
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Residues in contact with PRO 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B PHE* 4.2 19.8 - - + -
683B ALA 4.2 17.5 - - - +
684B PRO 5.4 0.2 - - - +
685B CYS* 4.0 20.4 - - + -
686B HIS* 6.6 0.2 - - + -
687B HIS* 4.7 3.1 - - + -
696B GLY 3.3 9.3 - - - +
697B CYS* 1.4 79.8 - - - +
699B CYS* 1.3 64.8 + - - +
701B SER* 4.2 1.3 - - - +
702B ALA* 2.8 46.2 + - + +
703B GLY 4.3 1.4 + - - -
707B VAL* 5.1 1.0 - - - +
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Residues in contact with CYS 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B ALA 5.3 1.1 - - - -
684B PRO* 4.9 2.2 - - - -
685B CYS* 3.7 20.9 - - - -
697B CYS* 3.3 3.2 - - - -
698B PRO* 1.3 79.1 - - - +
700B ALA* 1.3 60.0 + - - +
702B ALA 4.9 0.2 + - - -
703B GLY 5.5 0.9 + - - -
705B HIS 4.6 0.9 - - - +
706B PRO* 3.4 1.4 - - - +
707B VAL* 2.8 52.9 + - + +
708B LEU 4.6 3.1 - - - +
709B CYS* 3.7 22.9 - - - -
713B CYS* 3.6 31.0 - - - -
722B LEU* 4.9 0.4 - - + -
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Residues in contact with ALA 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B CYS 3.6 26.9 - - - +
692B THR* 3.8 18.4 - - - -
693B ALA* 4.0 3.8 - - - +
697B CYS* 3.3 9.7 + - + +
699B CYS* 1.3 81.3 - - - +
701B SER* 1.3 57.5 + - - +
705B HIS 4.6 0.5 - - - -
706B PRO* 3.6 31.6 - - + +
722B LEU* 3.8 9.6 - - + +
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Residues in contact with SER 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ALA* 3.8 30.8 + - - -
696B GLY* 4.3 5.0 - - - -
697B CYS 2.7 25.3 + - - -
698B PRO* 3.4 1.2 + - - +
700B ALA* 1.3 79.4 - - - +
702B ALA* 1.3 67.6 + - - +
703B GLY 3.3 12.1 - - - +
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Residues in contact with ALA 702 (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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680B GLU* 6.2 0.5 - - - -
682B PHE* 3.6 42.6 - - + -
698B PRO* 2.8 36.3 + - + +
701B SER* 1.3 76.2 + - - +
703B GLY* 1.3 57.5 + - - +
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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