Contacts of the helix formed by residues 194 - 200 (chain J) in PDB entry 6H25
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 194 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72J VAL* 3.9 19.1 - - + -
76J GLN* 4.0 26.7 - - - -
79J VAL* 5.6 5.6 - - - -
174J ILE* 3.8 13.2 - - + +
175J THR 2.8 16.6 + - - +
176J ASN* 4.0 8.7 - - - +
193J THR* 1.3 74.7 - - - +
195J GLU* 1.3 64.4 + - + +
197J TYR* 4.0 2.6 - - - +
198J VAL* 2.9 39.3 + - - +
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Residues in contact with GLU 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J ASN* 5.8 2.5 - - - +
193J THR* 3.4 5.2 + - - +
194J CYS* 1.3 79.8 - - + +
196J GLU* 1.3 61.8 + - + +
198J VAL* 3.3 8.8 - - + +
199J LYS* 2.9 42.9 + - + +
210J ARG* 5.5 11.1 - - + +
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Residues in contact with GLU 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J LYS* 4.6 10.0 + - - -
192J PHE* 4.7 13.8 - - + -
193J THR* 3.0 39.2 + - + +
195J GLU* 1.3 76.8 - - + +
197J TYR* 1.3 52.8 + - - +
199J LYS* 3.5 4.9 + - - +
200J SER* 2.7 40.0 + - - +
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Residues in contact with TYR 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J PRO* 5.8 1.7 - - - +
60J CYS* 6.4 1.3 - - + -
61J PRO* 4.5 16.8 - - + -
64J HIS* 3.2 27.8 + - - -
66J LEU* 3.7 34.6 - - + +
85J ILE* 5.8 7.4 - - + -
172J ILE* 5.2 3.6 - - + -
174J ILE* 4.3 18.8 - - + -
192J PHE* 4.4 20.3 - + + +
193J THR 3.4 18.7 + - - +
194J CYS* 4.0 2.2 - - - +
195J GLU 3.3 0.2 - - - -
196J GLU* 1.3 79.5 - - - +
198J VAL* 1.3 60.9 + - + +
200J SER* 4.1 6.3 - - - -
201J LEU* 2.9 65.3 + - + +
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Residues in contact with VAL 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J VAL* 4.0 28.3 - - + -
85J ILE* 5.7 1.1 - - + -
194J CYS* 2.9 27.9 + - - +
195J GLU* 3.3 18.4 - - + +
197J TYR* 1.3 79.9 - - + +
199J LYS* 1.3 72.4 + - + +
201J LEU* 4.4 9.6 + - + +
207J LEU* 3.5 35.3 - - + +
208J ILE* 4.6 6.2 - - + +
209J ASP 4.4 17.5 - - - +
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Residues in contact with LYS 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195J GLU* 2.9 28.6 + - + +
196J GLU* 3.8 4.9 - - - +
198J VAL* 1.3 90.1 - - + +
200J SER* 1.3 58.9 + - - +
201J LEU 3.3 5.0 + - - -
202J THR* 4.7 5.5 + - - -
204J ASN* 5.9 3.1 - - - +
208J ILE* 4.8 28.0 - - + +
209J ASP 5.6 3.0 + - - -
210J ARG* 6.1 2.4 - - - +
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Residues in contact with SER 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J SER 4.2 1.6 - - - +
59J VAL* 3.3 37.6 - - - +
60J CYS* 4.7 10.5 + - - -
61J PRO* 5.8 0.9 - - - +
196J GLU* 2.7 25.7 + - - +
197J TYR* 3.6 7.5 - - - -
199J LYS* 1.3 76.8 - - - +
201J LEU* 1.3 66.2 + - - +
202J THR* 4.8 0.4 - - - -
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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