Contacts of the helix formed by residues 194 - 199 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C VAL* 6.2 0.2 - - - -
192D LYS 3.8 2.0 + - - -
193D ARG* 1.3 79.2 - - - +
195D PRO* 1.3 76.0 - - + +
196D ASN* 3.2 15.0 + - - -
197D HIS* 3.3 19.0 + - - -
198D GLU* 3.2 17.2 + - - +
258D CYS* 3.3 6.9 - - - -
262D CYS* 4.0 7.4 - - + -
263D VAL 4.2 5.2 - - - +
264D GLY 3.6 7.2 - - - -
265D GLY* 3.5 21.4 - - - +
401D ZN 2.3 34.3 - - - -
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Residues in contact with PRO 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PRO* 4.3 6.5 - - + +
196C ASN* 4.0 29.8 - - - +
199C LEU* 5.2 10.5 - - + -
193D ARG 3.7 1.5 - - - +
194D CYS* 1.3 84.8 - - + +
196D ASN* 1.3 57.3 + - - +
198D GLU* 3.0 14.3 + - + +
199D LEU* 2.9 40.8 + - + +
264D GLY* 3.2 20.0 - - - +
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Residues in contact with ASN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C CYS* 3.7 1.8 - - - -
195C PRO* 3.5 21.6 - - - +
196C ASN* 2.9 50.6 + - - +
263C VAL* 2.8 43.5 + - + +
264C GLY* 4.6 3.9 - - - -
194D CYS* 3.3 11.9 - - - -
195D PRO* 1.3 75.0 - - - +
197D HIS* 1.3 59.6 + - - +
198D GLU 2.9 5.0 + - - -
199D LEU 3.4 1.4 + - - -
200D GLY* 3.0 22.9 + - - -
263D VAL 4.2 1.6 - - - +
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Residues in contact with HIS 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C VAL* 4.6 20.4 - - + +
155D ILE* 4.0 22.3 - - + +
193D ARG* 2.5 42.6 + - - +
194D CYS* 3.3 7.0 - - - -
196D ASN* 1.3 77.2 - - - +
198D GLU* 1.3 60.1 + - - +
200D GLY* 4.1 5.8 - - - +
202D ASP* 6.0 4.0 - - + -
203D PHE* 6.5 1.1 - + - -
204D ASN* 3.8 4.7 + - - -
257D MET 4.0 3.6 - - - -
258D CYS* 3.2 16.9 - - - -
259D ASN* 5.2 1.6 - - + -
262D CYS* 3.1 15.9 - - - -
401D ZN 2.0 34.8 - - - -
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Residues in contact with GLU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ARG* 4.5 8.7 - - + +
194D CYS 3.2 11.0 + - - +
195D PRO* 3.0 16.2 + - - +
196D ASN 2.9 0.2 - - - -
197D HIS* 1.3 76.5 - - - +
199D LEU* 1.3 67.6 + - - +
200D GLY 3.0 3.8 - - - -
204D ASN* 2.8 25.9 + - - +
211D ALA* 3.3 38.1 - - + +
212D SER* 4.2 17.6 + - - -
167L THR* 2.9 33.8 - - - +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PRO* 4.6 21.9 - - + +
199C LEU* 4.2 23.6 - - + -
195D PRO* 2.9 27.9 + - + +
196D ASN 3.6 3.6 - - - -
198D GLU* 1.3 91.2 - - + +
200D GLY* 1.3 56.7 + - - +
201D ARG 4.3 0.3 + - - -
164L LYS* 5.9 2.2 - - - +
166L SER* 3.7 39.5 - - - +
167L THR* 4.5 7.6 - - + -
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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