Contacts of the helix formed by residues 194 - 200 (chain L) in PDB entry 3VD1
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192L LYS 3.7 2.4 + - - -
193L ARG* 1.3 77.4 - - - +
195L PRO* 1.3 77.9 - - + +
196L ASN* 2.9 14.2 + - - -
197L HIS* 3.2 21.0 - - - -
198L GLU* 3.0 18.0 + - - +
258L CYS* 3.5 3.8 - - - -
262L CYS* 4.0 5.2 - - + -
263L VAL 4.1 7.6 - - - +
264L GLY 4.0 1.3 - - - -
265L GLY* 3.8 24.8 - - - +
401L ZN 2.3 34.1 - - - -
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Residues in contact with PRO 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196K ASN* 3.4 33.0 - - + +
193L ARG 3.6 2.6 - - - +
194L CYS* 1.3 84.6 - - + +
196L ASN* 1.3 64.0 + - - +
198L GLU* 3.1 11.6 + - + +
199L LEU* 3.0 37.9 + - + +
264L GLY* 3.4 23.6 - - - +
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Residues in contact with ASN 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K CYS* 3.8 12.3 - - - +
195K PRO* 4.9 4.0 - - - +
196K ASN* 2.8 46.8 + - - +
262K CYS* 5.2 1.6 - - - +
263K VAL* 2.7 46.0 + - + +
264K GLY* 5.0 7.5 - - - -
194L CYS* 2.9 10.6 + - - -
195L PRO* 1.3 80.2 - - - +
197L HIS* 1.3 64.2 + - + +
198L GLU 3.2 0.2 + - - -
199L LEU* 3.2 9.1 + - - +
200L GLY* 3.7 9.0 + - - -
263L VAL* 4.5 10.7 - - - +
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Residues in contact with HIS 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263K VAL* 4.8 23.5 - - + +
155L ILE* 3.7 24.2 - - + +
193L ARG* 2.9 26.4 + - - +
194L CYS* 3.1 8.0 + - - -
196L ASN* 1.3 79.1 - - + +
198L GLU* 1.3 61.8 + - - +
199L LEU 3.4 0.5 + - - -
200L GLY* 3.8 5.1 + - - +
202L ASP* 5.9 5.7 - - + +
203L PHE* 4.3 15.2 - + - -
204L ASN* 3.3 20.8 + - - +
257L MET 4.1 0.4 - - - -
258L CYS* 3.4 5.5 - - - -
259L ASN* 4.8 0.9 - - + -
262L CYS* 3.3 14.6 - - - -
401L ZN 2.0 37.4 - - - -
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Residues in contact with GLU 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L LYS* 5.7 2.6 - - - +
193L ARG* 3.7 17.3 - - + +
194L CYS 3.0 11.3 + - - +
195L PRO* 3.3 15.5 - - - +
196L ASN 3.1 0.2 - - - -
197L HIS* 1.3 79.3 - - - +
199L LEU* 1.3 73.6 + - + +
204L ASN* 2.9 16.7 + - - -
211L ALA* 3.6 33.8 - - + +
212L SER* 3.9 20.2 - - - -
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Residues in contact with LEU 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K PRO* 3.4 47.1 - - + +
199K LEU* 5.2 10.8 - - + -
195L PRO* 3.0 25.5 + - + +
196L ASN 3.2 2.3 + - - +
198L GLU* 1.3 101.5 - - + +
200L GLY* 1.3 61.4 + - - +
201L ARG* 5.9 0.2 - - - -
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Residues in contact with GLY 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K PRO* 5.7 1.3 - - - -
264K GLY* 5.6 8.7 - - - -
196L ASN 3.7 9.2 + - - -
197L HIS 3.8 4.1 + - - -
198L GLU 3.7 1.2 - - - -
199L LEU* 1.3 79.6 - - - +
201L ARG* 1.3 65.5 + - - -
202L ASP* 3.3 10.3 - - - -
204L ASN* 3.1 24.3 + - - +
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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