Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 4YVF
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 GLY 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLY 3.7 1.6 - - - -
221A TYR* 1.3 75.5 - - - +
223A ASP* 1.3 61.5 + - - -
224A VAL 3.4 1.3 - - - -
225A GLY 4.1 4.2 - - - +
226A LYS* 2.8 36.5 + - - +
248A ASN* 4.0 0.2 - - - -
275A THR* 4.9 0.2 + - - -
501A NAI 3.3 33.8 + - - -
430B TYR* 3.4 11.0 - - - -
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A SER* 4.6 7.6 - - - +
188A LYS* 4.1 17.7 + - - +
191A ASN* 3.4 33.0 + - + -
192A LEU* 3.3 28.4 - - + +
222A GLY* 1.3 69.3 - - - -
224A VAL* 1.3 66.3 + - - +
226A LYS* 3.4 8.2 + - - +
227A GLY 3.0 18.5 + - - -
501A NAI 3.2 15.2 + - - +
430B TYR* 4.1 8.5 + - - -
432B TYR 3.9 18.0 + - - +
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 3.6 13.7 - - + +
195A CYS* 3.9 12.6 - - - +
223A ASP* 1.3 75.3 - - - +
225A GLY* 1.3 64.8 + - - +
227A GLY* 3.2 2.8 + - - -
228A CYS* 3.0 27.4 + - - -
275A THR* 3.5 22.7 - - - -
299A ILE* 3.7 28.9 - - + +
501A NAI 2.8 66.1 + - + +
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 3.9 4.7 - - - +
220A GLY 3.5 16.8 - - - -
221A TYR* 4.2 4.3 - - - -
222A GLY 3.6 6.0 + - - +
223A ASP 3.3 0.2 - - - -
224A VAL* 1.3 80.3 - - - +
226A LYS* 1.3 60.8 + - - +
228A CYS* 3.3 1.4 + - - +
229A ALA* 2.9 26.3 + - - +
275A THR* 3.2 27.5 + - - -
501A NAI 4.2 0.2 + - - -
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LYS* 6.2 0.9 - - - +
192A LEU* 4.3 15.7 - - + -
221A TYR* 2.8 61.6 + - + +
222A GLY* 2.8 31.3 + - - +
223A ASP* 3.6 13.2 + - - +
225A GLY* 1.3 74.0 - - - +
227A GLY* 1.3 56.3 + - - +
229A ALA* 3.4 2.4 + - - +
230A GLN* 2.9 30.5 + - - +
248A ASN* 3.7 5.7 + - - -
251A GLN* 3.1 27.8 + - - +
257A TYR* 4.9 0.7 + - - -
430B TYR* 4.6 0.4 + - - -
432B TYR* 3.5 26.6 + - - +
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.6 33.5 - - - +
196A ARG* 3.2 21.8 - - - +
223A ASP 3.0 11.5 + - - -
224A VAL 3.2 2.7 + - - -
226A LYS* 1.3 77.4 - - - +
228A CYS* 1.3 56.6 + - - +
230A GLN* 3.4 0.8 + - - +
231A ALA* 2.9 25.6 + - - +
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Residues in contact with CYS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A CYS* 4.4 4.9 - - - -
199A LEU* 3.4 31.0 - - + -
218A VAL* 4.3 14.1 - - + -
224A VAL* 3.0 22.4 + - - +
225A GLY 3.7 3.4 - - - +
226A LYS 3.3 0.2 - - - -
227A GLY* 1.3 75.6 - - - +
229A ALA* 1.3 58.5 + - - +
231A ALA* 3.3 4.4 + - - +
232A LEU* 2.9 36.8 + - - +
273A VAL* 4.1 2.7 - - + -
275A THR* 4.0 4.0 - - - -
299A ILE* 3.7 39.0 - - - -
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 4.5 3.7 - - + +
221A TYR* 4.1 5.8 - - + -
225A GLY 2.9 18.4 + - - +
226A LYS 3.6 3.6 - - - +
228A CYS* 1.3 76.8 - - - +
230A GLN* 1.3 56.6 + - - +
233A ARG* 2.9 32.6 + - - +
239A VAL* 3.7 25.5 - - + +
241A ILE* 3.9 12.1 - - + -
257A TYR* 3.4 23.2 + - + +
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 4.1 9.5 - - - +
196A ARG* 2.7 31.6 + - - +
226A LYS 2.9 16.7 + - - +
227A GLY 3.7 4.5 - - - +
229A ALA* 1.3 74.4 - - - +
231A ALA* 1.3 65.7 + - - +
233A ARG* 3.4 5.6 + - - +
234A GLY* 3.0 20.1 + - - -
257A TYR* 3.5 11.2 + - - +
255B GLU* 3.0 28.7 + - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ARG* 3.4 33.1 - - + +
199A LEU* 5.0 3.6 - - + -
200A ILE* 4.0 19.5 - - + -
227A GLY 2.9 16.5 + - - +
228A CYS* 3.5 5.8 - - - +
230A GLN* 1.3 75.8 - - - +
232A LEU* 1.3 58.8 + - - +
234A GLY* 2.9 22.0 + - - -
235A PHE* 3.4 13.1 + - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 3.9 17.5 - - + -
200A ILE* 3.3 24.7 - - + -
203A ILE* 4.9 8.3 - - + -
211A ILE* 4.2 17.0 - - + -
216A ALA* 3.6 24.7 - - + -
218A VAL* 3.5 29.4 - - + -
228A CYS 2.9 20.0 + - - +
231A ALA* 1.3 76.1 - - - +
233A ARG* 1.3 62.6 + - - +
235A PHE* 3.0 13.2 + - - +
236A GLY 3.5 0.2 + - - -
237A ALA* 3.3 22.7 + - + +
239A VAL* 3.5 14.4 - - + -
271A ILE* 5.0 3.8 - - + -
273A VAL* 4.4 4.0 - - + -
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA 2.9 21.3 + - - +
230A GLN* 3.7 6.5 - - - +
232A LEU* 1.3 73.5 - - - +
234A GLY* 1.3 64.2 + - - +
235A PHE 3.1 1.0 + - - -
236A GLY* 3.2 12.6 + - - -
237A ALA 3.8 13.6 - - - +
239A VAL* 3.8 2.6 - - + +
255A GLU* 2.6 41.8 + - - +
256A GLY* 3.8 8.1 + - - -
257A TYR* 3.3 48.4 + - + +
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Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN 3.0 10.4 + - - -
231A ALA* 2.9 11.7 + - - -
233A ARG* 1.3 79.5 - - - +
235A PHE* 1.3 62.2 + - - +
236A GLY 3.4 0.2 - - - -
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ILE* 3.4 48.0 - - + -
204A LYS* 5.3 7.4 - - - -
211A ILE* 3.4 29.6 - - + -
212A ALA* 3.0 24.3 + - - +
231A ALA* 3.4 12.9 + - + -
232A LEU 3.0 3.9 + - - +
234A GLY* 1.3 81.4 - - - +
236A GLY* 1.3 59.5 + - - +
237A ALA 3.5 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