Contacts of the helix formed by residues 194 - 199 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K LYS 3.9 0.4 + - - -
193K ARG* 1.3 72.3 - - - +
195K PRO* 1.3 76.4 - - + +
196K ASN* 3.0 5.6 + - - -
197K HIS* 3.0 22.6 + - - -
198K GLU* 2.8 21.8 + - - +
258K CYS* 3.0 10.0 - - - -
262K CYS* 3.7 7.6 - - + -
263K VAL 3.8 15.5 - - - +
264K GLY 4.0 3.8 - - - -
265K GLY* 3.9 12.3 - - - -
401K ZN 2.3 34.8 - - - -
196L ASN* 3.8 8.1 - - - -
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Residues in contact with PRO 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K ARG 3.9 3.0 - - - +
194K CYS* 1.3 82.9 - - + +
196K ASN* 1.3 62.6 + - - +
198K GLU* 3.8 12.3 - - + +
199K LEU* 3.1 32.3 + - + +
263K VAL 4.8 0.9 - - - +
264K GLY* 3.2 25.1 - - - +
195L PRO 5.0 1.3 - - - +
196L ASN* 4.9 4.9 - - - +
199L LEU* 3.4 50.2 - - + +
200L GLY* 5.3 0.9 - - - +
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Residues in contact with ASN 196 (chain K).
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* 3.0 1.8 + - - -
195K PRO* 1.3 82.1 - - - +
197K HIS* 1.3 74.4 + - - +
199K LEU* 3.6 13.0 - - - +
262K CYS* 5.7 0.8 - - - -
195L PRO* 3.4 31.9 - - + +
196L ASN* 2.8 42.1 + - - +
263L VAL* 5.4 6.0 + - - +
264L GLY* 5.3 4.2 - - - -
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Residues in contact with HIS 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K ILE* 4.3 14.6 - - + +
193K ARG* 3.4 25.9 + - - +
194K CYS* 3.0 4.5 + - - -
196K ASN* 1.3 87.1 + - - +
198K GLU* 1.3 69.1 + - - +
199K LEU 3.0 8.1 - - - +
202K ASP* 4.9 18.6 - - + +
203K PHE* 5.6 4.0 - + - -
204K ASN* 3.8 2.8 + - - -
257K MET 4.5 9.2 - - - -
258K CYS* 3.6 9.9 - - - -
259K ASN* 4.0 14.4 - - - -
262K CYS* 2.7 25.9 - - - -
401K ZN 2.1 30.9 - - - -
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Residues in contact with GLU 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192K LYS* 5.5 2.6 - - - +
193K ARG* 4.1 11.5 - - + +
194K CYS 2.8 16.2 + - - +
195K PRO* 3.8 10.7 - - - +
197K HIS* 1.3 76.2 - - - +
199K LEU* 1.3 70.5 + - + +
204K ASN* 2.8 25.8 + - - -
211K ALA* 3.2 41.6 - - + +
212K SER* 3.9 22.8 + - - -
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Residues in contact with LEU 199 (chain K).
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* 3.1 21.6 + - + +
196K ASN* 3.6 11.2 - - - +
197K HIS 3.0 14.4 - - - +
198K GLU* 1.3 96.4 - - + +
200K GLY* 1.3 70.1 + - - +
202K ASP* 4.9 3.3 + - - +
199L LEU* 5.2 11.7 - - + -
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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