Contacts of the helix formed by residues 195 - 206 (chain B) in PDB entry 5VZ4
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 ASP 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B SER* 4.8 3.3 + - - -
132B LEU* 5.5 3.6 - - - +
192B ALA* 3.3 25.2 + - + +
194B SER* 1.3 76.5 + - - +
196B ILE* 1.3 59.7 + - - +
197B PRO* 3.4 14.2 - - - +
198B CYS* 3.2 32.1 + - + +
199B GLN* 2.8 33.2 + - - +
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Residues in contact with ILE 196 (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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94A THR* 3.6 23.1 - - - +
193B GLN 5.0 3.8 - - - +
194B SER 2.9 21.4 + - - +
195B ASP* 1.3 70.7 - - - +
197B PRO* 1.4 69.1 - - + +
199B GLN* 3.2 9.1 + - + +
200B GLN* 2.8 48.7 + - + +
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Residues in contact with PRO 197 (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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94A THR 4.8 0.9 - - - +
95A GLY* 4.6 11.9 - - - -
96A VAL* 3.8 17.6 - - + +
132B LEU* 4.1 20.6 - - + -
195B ASP* 3.4 11.0 - - - +
196B ILE* 1.4 92.7 - - + +
198B CYS* 1.3 63.1 + - - +
200B GLN* 3.3 16.0 + - - +
201B SER* 2.9 28.0 + - - -
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Residues in contact with CYS 198 (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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130B SER* 3.1 25.6 - - - +
131B CYS* 3.4 14.8 - - - +
132B LEU* 3.8 10.9 - - + +
190B ASP 3.6 0.7 - - - -
191B CYS* 2.1 56.8 - - + -
195B ASP* 3.2 29.6 + - - +
197B PRO* 1.3 78.4 - - - +
199B GLN* 1.3 57.9 + - - +
201B SER* 3.1 5.9 + - - -
202B LYS 2.9 23.9 + - - -
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Residues in contact with GLN 199 (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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191B CYS* 3.4 16.3 + - - +
192B ALA 3.1 26.3 + - - -
193B GLN* 3.8 25.6 + - - +
195B ASP 2.8 13.5 + - - +
196B ILE* 3.6 11.7 - - + +
198B CYS* 1.3 78.4 - - - +
200B GLN* 1.3 58.5 + - + +
202B LYS* 3.3 24.4 + - + +
203B GLU* 3.0 29.1 + - - +
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Residues in contact with GLN 200 (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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94A THR* 3.8 24.0 + - - -
95A GLY* 3.4 4.3 - - - -
96A VAL* 3.0 45.8 + - + +
97A SER* 5.7 0.7 - - - -
98A LEU* 5.3 1.5 - - - +
196B ILE* 2.8 38.0 + - + +
197B PRO* 3.3 12.2 - - - +
199B GLN* 1.3 78.3 - - + +
201B SER* 1.3 60.8 + - - +
203B GLU* 3.5 9.9 + - - +
204B ALA* 3.3 21.0 + - - +
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Residues in contact with SER 201 (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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96A VAL* 4.0 6.3 - - - +
98A LEU* 4.5 8.1 - - - +
131B CYS* 3.8 24.5 - - - -
132B LEU* 3.6 20.3 - - - +
135B ALA* 4.2 10.8 - - - +
197B PRO 2.9 15.4 + - - -
198B CYS 3.3 8.1 - - - -
200B GLN* 1.3 73.6 - - - +
202B LYS* 1.3 54.3 + - - +
204B ALA* 3.1 6.8 + - - +
205B LEU* 2.7 41.7 + - - +
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Residues in contact with LYS 202 (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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131B CYS* 3.9 19.7 - - - +
190B ASP* 2.7 27.4 + - - +
191B CYS* 4.2 7.2 - - - +
198B CYS 2.9 12.4 + - - +
199B GLN* 3.3 33.2 + - + +
201B SER* 1.3 74.6 - - - +
203B GLU* 1.3 65.5 + - - +
204B ALA 3.1 0.2 + - - -
205B LEU* 3.1 2.8 + - - -
206B HIS* 2.9 44.7 + - - +
208B LYS* 4.1 22.0 - - - +
313B ARG* 3.4 6.5 - - - +
402B SO4 2.6 29.2 + - - +
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Residues in contact with GLU 203 (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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199B GLN 3.0 16.4 + - - +
200B GLN* 3.7 10.1 - - - +
202B LYS* 1.3 77.6 - - - +
204B ALA* 1.3 63.2 + - + +
207B SER* 3.5 2.1 + - - -
208B LYS* 3.4 43.7 + - + +
209B THR* 3.8 24.8 + - + +
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Residues in contact with ALA 204 (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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98A LEU* 3.8 33.4 - - + +
151B TYR* 3.6 1.2 + - - -
152B LEU* 3.5 23.6 - - + +
200B GLN 3.3 10.2 + - - +
201B SER* 3.1 7.9 + - - +
203B GLU* 1.3 79.9 - - - +
205B LEU* 1.3 64.3 + - - +
206B HIS 3.2 1.4 + - - -
207B SER* 3.3 12.0 + - - -
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Residues in contact with LEU 205 (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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98A LEU* 4.3 10.5 - - + -
131B CYS 3.7 24.0 - - - +
134B VAL* 4.8 0.7 - - + -
135B ALA* 3.9 15.9 - - + +
148B LEU* 3.8 35.7 - - + -
151B TYR* 2.6 25.4 + - + -
175B TYR* 4.9 4.7 + - - -
186B LEU* 3.9 31.3 - - + +
189B CYS* 4.4 14.8 - - - -
201B SER 2.7 23.0 + - - +
202B LYS* 4.0 3.1 - - - +
204B ALA* 1.3 74.1 - - - +
206B HIS* 1.3 70.0 + - + +
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Residues in contact with HIS 206 (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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151B TYR* 3.4 1.8 - - - -
175B TYR* 4.8 7.4 - - - -
186B LEU* 2.8 30.1 + - + -
187B ALA* 4.0 4.8 + - - -
189B CYS* 3.8 20.4 - - - -
202B LYS* 2.9 33.1 + - + +
205B LEU* 1.3 92.3 - - + +
207B SER* 1.3 71.0 + - - +
208B LYS* 3.2 18.4 + - + +
212B VAL* 3.7 15.5 - - + +
288B GLN* 4.0 10.9 + - - +
313B ARG* 3.7 27.3 + - - -
402B SO4 5.6 0.2 + - - -
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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