Contacts of the helix formed by residues 219 - 231 (chain A) in PDB entry 5PJP
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 HIS 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A CYS* 5.0 4.0 - - - -
215A VAL* 3.7 10.3 - - + +
216A PRO* 2.8 23.2 + - + +
218A GLU* 1.3 113.9 + - + +
220A GLY* 1.4 63.4 + - - +
221A GLN* 3.2 3.6 - - - -
222A ARG* 2.9 52.6 + - - +
223A LEU 3.6 2.8 + - - -
260A PRO* 3.6 34.3 - - + +
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Residues in contact with GLY 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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215A VAL* 4.2 5.4 - - - -
216A PRO 3.3 5.5 + - - -
217A PRO 3.1 9.1 + - - -
218A GLU 3.6 0.6 - - - -
219A HIS* 1.4 78.5 - - - +
221A GLN* 1.3 62.2 + - - +
223A LEU* 3.1 7.4 + - - +
224A GLU* 3.1 22.5 + - - +
277A TYR* 3.4 23.5 - - - -
279A TYR* 3.8 15.6 - - - -
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Residues in contact with GLN 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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218A GLU 5.4 1.2 + - - +
219A HIS* 3.2 1.2 + - - +
220A GLY* 1.3 76.5 - - - +
222A ARG* 1.3 57.3 + - + +
224A GLU* 3.6 16.6 + - - +
225A ARG* 3.0 29.1 + - - +
228A ARG* 5.2 0.7 + - - -
277A TYR* 3.4 18.0 + - + +
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Residues in contact with ARG 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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219A HIS* 2.9 41.1 + - - +
221A GLN* 1.3 79.1 - - + +
223A LEU* 1.3 62.1 + - - +
225A ARG* 3.4 7.9 + - - +
226A LEU 3.1 17.3 + - - -
258A GLY 4.4 13.3 + - - -
259A ILE* 3.6 23.5 - - + +
260A PRO* 3.9 23.6 - - + +
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Residues in contact with LEU 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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191A TRP* 3.8 26.0 - - + -
215A VAL* 4.1 18.6 - - + -
219A HIS 3.6 1.8 + - - -
220A GLY 3.1 10.6 + - - +
222A ARG* 1.3 79.6 - - - +
224A GLU* 1.3 57.4 + - - +
226A LEU* 3.2 5.6 + - + +
227A ALA* 2.8 28.3 + - - +
242A LEU* 4.8 5.4 - - + -
249A ILE* 4.2 15.9 - - + -
254A LEU* 3.8 29.4 - - + -
259A ILE* 4.4 10.9 - - + +
279A TYR* 3.6 41.1 - - + -
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Residues in contact with GLU 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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220A GLY 3.1 14.4 + - - +
221A GLN* 3.6 18.3 + - - +
222A ARG 3.3 0.2 - - - -
223A LEU* 1.3 76.5 - - - +
225A ARG* 1.3 57.2 + - - +
227A ALA* 3.2 7.2 + - - +
228A ARG* 2.9 56.3 + - - +
241A PHE* 5.4 0.2 - - - -
242A LEU* 4.4 6.7 - - + -
277A TYR* 2.7 31.5 + - - -
279A TYR* 2.6 32.0 + - + +
308A SER* 5.3 2.4 + - - -
407A EDO 3.2 20.1 + - - +
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Residues in contact with ARG 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 GLN 3.0 15.6 + - - +
222A ARG* 3.7 6.7 - - - +
223A LEU 3.2 0.2 - - - -
224A GLU* 1.3 77.2 - - - +
226A LEU* 1.3 61.9 + - - +
228A ARG* 3.3 16.6 + - - +
229A GLU* 3.2 39.9 + - + +
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Residues in contact with LEU 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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222A ARG 3.1 11.1 + - - +
223A LEU* 3.7 7.2 - - + +
225A ARG* 1.3 78.3 - - - +
227A ALA* 1.3 62.5 + - - +
229A GLU* 3.0 20.8 + - + +
230A LEU* 2.9 51.1 + - + +
249A ILE* 4.4 7.6 - - + -
253A VAL 4.6 0.9 - - - +
254A LEU* 4.0 17.3 - - + -
257A ASN* 3.6 37.2 - - + +
259A ILE* 3.7 28.5 - - + -
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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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223A LEU* 2.8 17.4 + - + +
224A GLU 3.5 4.7 - - - +
226A LEU* 1.3 77.6 - - - +
228A ARG* 1.3 56.7 + - - +
230A LEU* 4.6 0.2 - - - -
231A PHE* 2.9 41.4 + - + -
241A PHE* 3.5 21.2 - - + -
242A LEU* 4.1 23.8 - - + -
249A ILE* 4.4 13.9 - - + +
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Residues in contact with ARG 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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221A GLN 5.2 0.4 + - - -
224A GLU* 2.9 51.2 + - - +
225A ARG* 3.7 14.0 - - - +
226A LEU 3.2 0.2 - - - -
227A ALA* 1.3 76.3 - - - +
229A GLU* 1.3 61.8 + - + +
232A PRO* 3.5 23.7 - - - +
235A SER* 3.2 33.1 + - - +
239A GLY* 3.6 25.3 + - - -
241A PHE* 4.2 8.1 - - + -
407A EDO 4.6 9.8 + - - -
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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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225A ARG* 3.2 33.5 + - + +
226A LEU* 3.0 28.4 + - + +
228A ARG* 1.3 79.7 - - + +
230A LEU* 1.3 62.1 + - + +
232A PRO* 3.6 14.1 - - - +
257A ASN* 4.8 3.3 - - - +
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Residues in contact with LEU 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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82A ARG* 4.8 11.3 + - - +
85A VAL* 4.0 28.0 - - + +
226A LEU* 2.9 47.9 + - + +
227A ALA* 4.6 0.2 - - - -
229A GLU* 1.3 76.2 - - + +
231A PHE* 1.3 78.9 + - + +
232A PRO* 3.3 8.5 - - - +
249A ILE* 3.9 30.3 - - + -
253A VAL* 4.1 10.8 - - + -
257A ASN* 5.4 2.2 - - - +
411A EDO 4.9 2.6 + - - -
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Residues in contact with PHE 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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85A VAL* 3.6 25.4 - - + -
86A PHE 3.8 9.9 - - - -
87A THR* 3.6 26.5 - - + -
227A ALA* 2.9 21.9 + - + +
228A ARG 3.8 2.2 - - - -
230A LEU* 1.3 88.0 - - + +
232A PRO* 1.4 65.1 - - - +
233A GLY 3.4 2.0 - - - -
234A SER* 3.2 12.0 + - - +
235A SER* 3.0 21.5 + - - -
241A PHE* 3.8 24.0 - + + -
247A ALA* 3.8 15.3 - - + -
248A LEU 3.6 17.0 - - - -
249A ILE* 3.9 20.6 - - + -
411A EDO 3.7 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