Contacts of the helix formed by residues 220 - 234 (chain A) in PDB entry 2R5N
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 4.5 5.7 + - - +
217A ASP* 3.1 25.8 + - - +
218A GLY 3.5 1.0 - - - -
219A HIS* 1.3 79.3 - - - +
221A ALA* 1.3 65.7 + - - +
222A ALA* 3.7 12.0 + - - +
223A SER* 2.7 36.5 + - - +
224A ILE* 3.0 25.3 + - - +
226A ARG* 4.9 0.7 + - - -
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Residues in contact with ALA 221 (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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4A ARG* 3.6 39.3 - - + +
5A LYS* 5.2 3.3 - - + +
35A ASP* 5.3 5.2 - - + +
38A GLU* 4.6 1.1 - - - +
39A VAL* 3.6 21.4 - - + +
219A HIS 4.1 2.0 + - - -
220A ASP* 1.3 73.5 + - - +
222A ALA* 1.3 57.0 + - - +
224A ILE* 3.2 7.6 + - - +
225A LYS* 2.8 31.1 + - - +
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Residues in contact with ALA 222 (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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220A ASP* 3.2 12.3 + - - +
221A ALA* 1.3 77.9 - - - +
223A SER* 1.3 57.9 + - - +
225A LYS* 3.4 6.8 + - - +
226A ARG* 3.0 46.3 + - + +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 4.1 6.0 - - - +
217A ASP* 4.0 26.8 - - - +
220A ASP* 2.7 30.3 + - - +
222A ALA* 1.3 71.5 - - - +
224A ILE* 1.3 66.1 + - - +
226A ARG* 3.2 30.6 + - - +
227A ALA* 3.1 23.2 + - - +
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Residues in contact with ILE 224 (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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35A ASP* 3.9 8.5 - - + +
36A ILE* 3.9 42.2 - - + +
39A VAL* 3.9 19.7 - - + -
40A LEU 5.4 0.2 - - - +
181A PHE* 4.5 4.7 - - + -
216A ILE* 4.2 13.0 - - + -
217A ASP 3.7 9.2 - - - +
218A GLY* 3.5 25.8 - - - +
220A ASP 3.0 22.8 + - - +
221A ALA* 3.6 7.4 - - - +
223A SER* 1.3 76.6 - - - +
225A LYS* 1.3 63.3 + - - +
227A ALA* 3.1 4.8 + - + +
228A VAL* 2.9 31.9 + - + +
241A LEU* 5.8 0.7 - - + -
243A CYS* 5.5 2.2 - - - -
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Residues in contact with LYS 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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4A ARG* 4.5 8.8 - - - +
39A VAL* 3.8 15.0 - - + +
43A ASP* 2.9 31.0 + - - +
44A PHE* 3.9 16.8 - - + -
221A ALA 2.8 17.9 + - - +
222A ALA* 3.7 6.5 - - - +
224A ILE* 1.3 77.6 - - - +
226A ARG* 1.3 63.2 + - + +
228A VAL* 3.2 2.8 + - - +
229A GLU* 3.0 50.9 + - - +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 4.9 0.4 + - - -
222A ALA* 3.0 39.3 + - - +
223A SER* 3.2 33.4 + - - +
224A ILE 3.3 0.2 - - - -
225A LYS* 1.3 76.1 - - - +
227A ALA* 1.3 58.7 + - - +
229A GLU* 3.3 16.3 + - - +
230A GLU* 3.0 28.9 + - - +
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Residues in contact with ALA 227 (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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213A ILE* 3.2 22.6 - - + +
216A ILE* 3.5 33.7 - - + -
223A SER 3.1 13.0 + - - +
224A ILE* 3.1 10.3 + - - +
226A ARG* 1.3 75.1 - - - +
228A VAL* 1.3 64.6 + - - +
230A GLU* 3.2 3.5 + - - -
231A ALA* 3.0 21.0 + - - +
241A LEU* 3.6 10.5 - - + -
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Residues in contact with VAL 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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39A VAL* 4.9 1.6 - - + -
40A LEU* 5.2 2.9 - - + -
44A PHE* 3.7 34.8 - - + -
150A TYR* 4.7 13.0 - - + -
179A ILE* 5.2 2.2 - - + -
181A PHE* 3.7 33.9 - - + -
224A ILE* 2.9 26.0 + - + +
225A LYS 3.7 6.3 - - - +
227A ALA* 1.3 74.7 - - - +
229A GLU* 1.3 55.4 + - - +
231A ALA* 3.3 4.4 + - - +
232A ARG* 2.9 50.3 + - + +
241A LEU* 4.0 5.8 - - + -
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Residues in contact with GLU 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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44A PHE* 3.7 16.3 - - + -
225A LYS* 3.0 47.3 + - - +
226A ARG* 3.6 18.7 - - - +
227A ALA 3.3 0.2 - - - -
228A VAL* 1.3 76.8 - - - +
230A GLU* 1.3 55.1 + - - +
232A ARG* 3.3 10.3 + - - +
233A ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 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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211A HIS* 2.8 33.3 + - + +
212A VAL 5.1 0.3 - - - +
213A ILE* 3.7 25.3 - - + +
226A ARG 3.0 14.5 + - - +
227A ALA* 3.5 9.1 - - - +
229A GLU* 1.3 75.5 - - - +
231A ALA* 1.3 62.7 + - - +
233A ALA* 3.0 16.4 + - - +
234A VAL* 3.2 15.8 + - + +
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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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176A GLY 4.5 3.3 - - - +
179A ILE* 3.8 20.8 - - + +
211A HIS* 5.1 0.9 - - - -
213A ILE* 4.0 3.7 - - + +
227A ALA 3.0 16.1 + - - +
228A VAL* 3.6 5.6 - - - +
230A GLU* 1.3 74.7 - - - +
232A ARG* 1.3 62.2 + - - +
234A VAL* 3.2 21.8 + - - +
239A SER* 3.5 35.7 + - - +
241A LEU* 3.9 13.9 - - + -
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Residues in contact with ARG 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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44A PHE* 3.6 41.8 + - - +
58A ASP* 5.4 1.0 + - - -
148A TYR* 3.3 51.3 + - - +
150A TYR* 2.9 22.3 + - - -
179A ILE* 3.8 18.2 - - + -
228A VAL* 2.9 26.6 + - + +
229A GLU* 3.6 6.1 - - - +
231A ALA* 1.3 76.4 - - - +
233A ALA* 1.3 61.2 + - - +
234A VAL 3.5 3.3 + - - +
235A THR* 4.3 9.0 - - - +
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Residues in contact with ALA 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 GLU 3.0 12.4 + - - +
230A GLU* 3.0 12.5 + - - +
232A ARG* 1.3 76.2 - - - +
234A VAL* 1.3 64.1 + - + +
235A THR* 3.4 12.0 + - - +
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Residues in contact with VAL 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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176A GLY 3.6 11.8 - - - +
211A HIS* 3.7 52.0 - - + +
230A GLU* 3.2 15.1 + - + +
231A ALA 3.2 15.8 - - - +
232A ARG 3.3 2.7 - - - +
233A ALA* 1.3 76.7 - - + +
235A THR* 1.3 59.3 + - - +
236A ASP* 3.5 20.0 - - - +
237A LYS* 3.8 18.2 - - + +
239A SER* 4.5 1.6 - - - +
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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