Contacts of the helix formed by residues 222 - 238 (chain A) in PDB entry 1YPN
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 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 ASN* 3.6 13.1 + - - +
221A HIS* 1.3 72.4 - - - +
223A GLU* 1.3 58.5 + - + +
225A ALA* 3.2 9.9 + - + +
226A LEU* 3.0 59.0 + - + +
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Residues in contact with GLU 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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221A HIS* 3.3 25.3 + - + +
222A HIS* 1.3 76.9 - - + +
224A THR* 1.3 66.7 + - - +
226A LEU* 3.3 12.8 + - - +
227A ARG* 3.2 39.0 + - - +
252A LEU* 3.7 35.0 - - + +
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Residues in contact with THR 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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98A ILE* 3.9 11.4 - - + -
99A CYS 3.3 22.9 - - - +
101A ARG* 3.2 35.9 + - + +
200A ALA* 4.1 2.2 - - + -
221A HIS* 2.7 34.4 + - - -
223A GLU* 1.3 76.3 + - - +
225A ALA* 1.3 66.4 + - - +
227A ARG* 3.4 10.9 + - - +
228A VAL* 3.0 31.4 + - + +
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Residues in contact with ALA 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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98A ILE* 3.9 26.5 - - + +
220A ASN* 4.2 18.2 - - - +
221A HIS 3.0 11.0 + - - +
222A HIS* 3.5 12.3 - - + +
223A GLU 3.2 0.4 - - - -
224A THR* 1.3 77.2 - - - +
226A LEU* 1.3 57.6 + - + +
228A VAL* 3.2 1.7 + - - +
229A THR* 2.8 37.5 + - - +
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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 HIS* 3.0 51.9 + - + +
223A GLU* 3.5 13.0 - - + +
224A THR 3.3 0.2 - - - -
225A ALA* 1.3 77.5 - - - +
227A ARG* 1.3 61.2 + - - +
229A THR* 3.5 6.2 + - - -
230A ALA* 3.4 20.8 + - - +
252A LEU* 4.3 11.0 - - + -
257A ILE* 4.0 13.9 - - + +
280A PRO* 3.9 45.1 - - + +
281A GLN* 5.7 0.7 - - - -
283A ALA* 3.9 7.6 - - + +
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Residues in contact with ARG 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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101A ARG* 3.6 51.9 + - - +
102A GLU 5.6 0.6 + - - -
104A PRO* 5.1 4.2 - - - +
223A GLU* 3.2 28.0 + - - +
224A THR* 3.7 11.0 + - - +
225A ALA 3.3 0.2 - - - -
226A LEU* 1.3 77.4 - - - +
228A VAL* 1.3 60.7 + - - +
230A ALA* 3.5 1.0 + - - +
231A GLU* 3.0 28.8 + - - +
249A TYR* 3.9 19.6 + - - -
250A ALA* 3.1 35.8 + - - +
251A GLU* 3.6 17.5 + - - +
252A LEU* 3.7 20.4 - - + +
257A ILE* 4.2 4.9 - - + -
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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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82A MET* 3.6 32.3 - - + -
98A ILE* 4.3 15.5 - - + -
101A ARG* 4.0 15.3 - - - +
196A VAL* 4.9 0.2 - - + -
197A GLY* 4.3 19.5 - - - +
200A ALA* 4.6 4.3 - - + -
224A THR* 3.0 33.3 + - + +
225A ALA 4.0 2.0 - - - +
227A ARG* 1.3 75.0 - - - +
229A THR* 1.3 61.2 + - - +
231A GLU* 3.9 7.4 - - - +
232A ARG* 2.8 35.9 + - + +
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Residues in contact with THR 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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98A ILE* 4.8 6.5 - - - +
225A ALA* 2.8 31.4 + - - +
226A LEU* 3.8 6.2 - - - -
228A VAL* 1.3 71.8 - - - +
230A ALA* 1.3 58.8 + - - +
232A ARG* 3.7 5.4 - - - +
233A ALA* 2.8 28.8 + - - +
283A ALA* 4.6 5.2 - - + -
284A GLU* 4.4 27.6 - - + +
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Residues in contact with ALA 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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226A LEU 3.4 5.3 + - - +
227A ARG 3.8 7.9 - - - +
228A VAL 3.3 0.2 - - - -
229A THR* 1.3 79.4 - - - +
231A GLU* 1.3 61.6 + - - +
233A ALA* 3.2 3.3 + - - +
234A MET* 3.1 22.3 + - - +
250A ALA* 4.6 1.8 - - + -
257A ILE* 4.1 19.5 - - + -
259A LEU* 3.9 12.7 - - + +
283A ALA* 3.5 37.0 - - + +
286A MET* 4.7 0.9 - - + -
287A GLY* 3.8 5.0 - - - -
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Residues in contact with GLU 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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101A ARG* 2.7 33.7 + - - -
196A VAL* 3.8 10.5 - - + +
197A GLY* 3.0 27.9 + - - -
227A ARG 3.0 16.9 + - - +
228A VAL* 3.7 7.0 - - - +
230A ALA* 1.3 75.1 - - - +
232A ARG* 1.3 59.0 + - - +
234A MET* 3.3 1.7 - - - +
235A ASN* 3.2 22.0 + - - +
248A SER* 3.0 34.1 + - - +
249A TYR 4.0 1.3 - - - -
250A ALA* 2.8 38.7 + - + +
259A LEU* 4.1 3.8 - - + -
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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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82A MET* 3.3 29.5 + - - +
85A VAL* 3.4 33.2 + - - +
86A PRO 3.0 22.2 + - - -
87A VAL* 3.7 21.6 + - + +
89A PHE* 3.3 24.4 - - - -
95A LEU* 5.3 4.6 - - - +
98A ILE* 6.0 1.1 - - - -
196A VAL* 3.5 23.8 - - + +
228A VAL* 2.8 20.8 + - + +
229A THR* 3.9 5.2 - - - +
231A GLU* 1.3 73.3 - - - +
233A ALA* 1.3 56.7 + - - +
234A MET 3.1 1.6 - - - -
235A ASN* 3.7 4.2 - - + +
236A THR* 2.7 42.2 + - - +
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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 THR 2.8 22.0 + - - +
230A ALA 3.2 5.4 + - - +
232A ARG* 1.3 71.4 - - - +
234A MET* 1.3 64.6 + - - +
236A THR* 3.5 6.0 + - - -
237A ARG* 3.3 22.2 + - - +
284A GLU* 3.1 46.2 - - + +
287A GLY* 4.1 4.5 - - - -
288A ILE* 4.0 9.5 - - + +
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Residues in contact with MET 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 ALA 3.1 9.4 + - - +
231A GLU 3.3 11.4 - - - +
233A ALA* 1.3 81.5 - - - +
235A ASN* 1.3 70.1 + - - +
237A ARG 3.4 0.5 + - - -
238A LEU* 3.2 41.8 + - + +
246A ILE* 3.9 9.6 - - + -
247A GLY 3.9 11.2 - - - +
248A SER* 4.0 6.3 - - - +
259A LEU* 4.3 4.9 - - + -
261A ALA* 3.6 33.2 - - + -
262A LEU 5.1 0.4 - - - +
287A GLY* 3.2 22.2 + - - +
290A LEU* 4.2 11.2 - - + -
291A ALA* 3.4 27.1 - - - +
294A LEU* 4.9 3.8 - - + -
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Residues in contact with ASN 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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87A VAL* 4.3 11.3 - - + +
196A VAL* 3.8 25.0 - - + +
231A GLU 3.2 6.2 + - - +
232A ARG* 3.3 10.1 + - - +
234A MET* 1.3 82.5 - - - +
236A THR* 1.3 51.6 + - - +
238A LEU* 3.1 6.3 + - - -
239A GLU 2.7 30.0 + - - -
240A GLY* 3.3 28.9 + - - -
241A GLY* 4.8 5.5 + - - +
246A ILE* 3.6 23.1 - - - +
248A SER* 3.4 26.7 - - - -
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Residues in contact with THR 236 (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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87A VAL* 3.3 37.2 + - + +
88A GLU* 5.5 2.9 - - - +
232A ARG* 2.7 32.6 + - - +
233A ALA* 3.9 7.0 - - - -
235A ASN* 1.3 73.0 - - - +
237A ARG* 1.3 60.8 + - - +
239A GLU* 3.2 25.7 + - - +
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Residues in contact with ARG 237 (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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233A ALA 3.3 10.6 + - - +
235A ASN 3.3 0.6 - - - -
236A THR* 1.3 76.8 - - - +
238A LEU* 1.3 59.7 + - - +
239A GLU* 3.1 5.3 + - - +
288A ILE* 4.2 18.4 - - + +
291A ALA* 3.6 27.4 - - + -
292A GLU* 3.2 37.5 + - + +
295A LEU* 3.6 27.5 - - + +
300A ARG* 4.4 11.7 - - - +
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Residues in contact with LEU 238 (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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234A MET* 3.2 36.2 + - + +
235A ASN 3.1 8.2 + - - +
237A ARG* 1.3 78.2 - - - +
239A GLU* 1.3 70.2 + - - +
240A GLY* 3.1 2.1 + - - -
246A ILE* 3.6 27.3 - - + +
263A VAL* 3.8 17.9 - - + -
291A ALA* 3.5 38.4 - - + +
294A LEU* 4.9 5.4 - - + -
295A LEU* 4.0 19.3 - - + -
299A ALA* 5.4 0.7 - - + -
303A LEU* 4.2 21.5 - - + +
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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