Contacts of the helix formed by residues 219 - 228 (chain A) in PDB entry 4ED6
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 ASN 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLY 4.7 2.6 + - - +
7A ARG* 3.7 8.3 - - - +
9A VAL* 4.0 11.2 - - - +
217A SER* 3.5 1.3 + - - -
218A HIS* 1.3 83.9 - - - +
220A LYS* 1.3 59.2 + - - +
221A VAL* 3.3 8.3 + - - +
222A LEU* 3.0 41.8 + - - +
223A ALA* 3.1 29.1 + - - +
301A MET* 4.2 0.6 - - - +
304A GLY 3.1 27.9 + - - -
305A ILE* 4.2 0.4 - - - +
306A GLU* 3.4 40.6 - - - +
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Residues in contact with LYS 220 (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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7A ARG* 4.9 1.3 - - - +
9A VAL* 4.0 10.5 - - + -
110A GLU* 2.6 37.4 + - - -
118A TYR* 3.3 40.5 - - + -
219A ASN* 1.3 73.5 - - - +
221A VAL* 1.3 60.4 + - - +
223A ALA* 3.5 0.4 - - - +
224A LYS* 2.9 31.5 + - - +
256A ARG* 3.9 17.7 - - - +
306A GLU* 3.8 5.8 + - - +
308A ASP* 2.9 41.8 + - - +
309A PRO 3.4 8.3 + - - +
310A VAL* 3.7 18.8 - - + -
311A LYS* 5.4 1.8 - - - +
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Residues in contact with VAL 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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219A ASN* 3.3 2.5 + - - +
220A LYS* 1.3 76.4 - - - +
222A LEU* 1.3 62.8 + - + +
224A LYS* 3.5 5.8 + - - +
225A LEU* 2.8 29.1 + - + +
247A PHE* 5.9 0.7 - - + -
255A ILE* 4.0 25.6 - - + -
256A ARG* 4.5 28.3 + - + +
297A TRP* 4.0 11.9 - - + -
301A MET* 3.5 31.9 - - + -
306A GLU* 3.4 28.4 + - - +
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Residues in contact with LEU 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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217A SER* 3.3 27.1 - - - +
218A HIS* 5.1 3.6 - - + +
219A ASN* 3.0 22.2 + - - +
221A VAL* 1.3 75.3 - - + +
223A ALA* 1.3 56.7 + - - +
225A LEU* 3.6 9.7 - - + +
226A ALA* 2.7 36.6 + - - +
238A VAL* 4.6 15.5 - - + +
239A SER 5.4 0.7 - - - +
240A HIS* 5.5 3.6 - - - -
243A VAL* 4.1 20.4 - - + -
246A LEU* 5.5 0.2 - - + -
247A PHE* 3.8 33.0 - - + -
301A MET* 4.5 8.1 - - + -
304A GLY* 3.6 23.6 - - - +
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Residues in contact with ALA 223 (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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9A VAL* 3.7 20.9 - - + +
10A ALA 4.0 2.0 - - - -
11A LEU* 3.8 22.2 - - + +
215A GLY* 3.4 14.8 - - - +
217A SER* 3.8 8.2 - - - +
219A ASN 3.1 20.0 + - - +
220A LYS* 3.5 7.9 - - - +
221A VAL 3.3 0.2 - - - -
222A LEU* 1.3 76.7 - - - +
224A LYS* 1.3 57.3 + - - +
226A ALA* 3.1 1.4 + - - -
227A CYS* 2.8 27.4 + - - +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.6 27.2 - - + +
13A ASP* 4.9 2.0 + - - -
116A GLU* 3.0 34.6 + - - +
118A TYR* 3.6 16.4 - - - +
220A LYS 2.9 19.4 + - - +
221A VAL* 3.7 5.2 - - - +
223A ALA* 1.3 74.6 - - - +
225A LEU* 1.3 64.9 + - - +
227A CYS* 3.2 15.6 + - + +
228A GLY* 3.6 4.0 + - - -
256A ARG* 4.4 26.0 - - + -
7P A 4.8 3.0 + - - -
8P T 3.9 24.2 + - - -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A VAL* 2.8 23.7 + - + +
222A LEU* 3.6 10.8 - - + +
224A LYS* 1.3 75.9 - - - +
226A ALA* 1.3 65.0 + - - +
228A GLY* 3.3 9.4 + - - -
229A LEU* 3.6 16.4 + - + +
238A VAL* 6.1 0.4 - - + -
246A LEU* 3.9 20.2 - - + -
247A PHE* 3.6 32.3 - - + -
250A MET* 4.2 26.0 - - + -
254A LYS* 4.0 23.3 - - + +
255A ILE* 4.4 12.8 - - + -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLY* 3.9 4.7 - - - -
216A ILE 4.4 2.5 - - - +
222A LEU 2.7 21.7 + - - +
223A ALA* 3.5 5.2 - - - +
225A LEU* 1.3 69.5 - - - +
227A CYS* 1.3 68.0 + - - +
229A LEU* 3.0 29.1 + - - +
236A THR* 3.4 28.6 - - - +
238A VAL* 3.3 27.3 - - + +
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Residues in contact with CYS 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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11A LEU* 3.7 35.0 - - + -
13A ASP* 3.9 14.4 - - - -
213A SER* 3.7 13.5 - - - -
214A ALA* 3.7 19.5 - - - +
215A GLY* 3.5 17.9 - - - +
223A ALA 2.8 13.5 + - - +
224A LYS 3.2 11.1 + - - +
226A ALA* 1.3 73.6 - - - +
228A GLY* 1.3 60.8 + - - +
229A LEU 3.4 0.3 + - - -
230A ASN 4.0 6.9 + - - +
231A LYS* 3.8 17.1 - - - +
234A ARG 5.1 0.2 - - - +
235A GLN* 6.0 0.2 - - - -
236A THR* 5.0 0.7 + - - -
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LYS 3.6 4.2 + - - -
225A LEU 3.3 8.5 + - - -
226A ALA 3.1 1.2 + - - -
227A CYS* 1.3 78.5 - - - +
229A LEU* 1.3 63.0 + - - +
230A ASN* 3.3 1.6 + - - -
231A LYS* 4.3 22.2 + - - +
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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