Contacts of the helix formed by residues 247 - 263 (chain A) in PDB entry 4ZGY
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 LYS 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A SER 5.2 0.4 - - - +
242A GLU* 3.2 47.8 - - - +
244A VAL* 2.6 29.9 + - + +
245A LYS* 3.2 14.1 + - - +
246A LEU* 1.3 76.1 - - - +
248A PHE* 1.3 65.2 + - - +
249A GLU* 3.4 6.1 - - + +
250A GLU* 3.2 36.3 + - + +
251A ILE* 3.1 20.3 + - - +
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Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 4.0 13.1 - - - +
55A TRP* 3.7 33.0 - + - -
58A ALA* 3.5 26.5 - - + -
59A LEU* 4.3 2.9 - - + -
238A PHE* 3.9 20.0 - + + -
239A PRO* 3.7 20.8 - - + +
242A GLU* 5.4 1.4 + - - +
247A LYS* 1.3 72.5 - - - +
249A GLU* 1.3 80.1 + - - +
251A ILE* 3.0 6.6 + - - +
252A THR* 2.9 52.2 + - + +
278A TYR* 3.5 47.1 - + + -
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 2.5 59.8 + - - +
58A ALA* 4.9 7.3 - - + +
242A GLU* 4.6 1.9 - - - +
247A LYS* 3.4 4.0 - - + +
248A PHE* 1.3 81.0 + - + +
250A GLU* 1.3 58.6 + - + +
252A THR* 3.1 10.7 + - - +
253A GLY* 2.9 27.9 + - - -
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Residues in contact with GLU 250 (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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205A PRO* 4.6 2.3 - - - +
245A LYS* 3.8 10.7 + - - +
246A LEU* 3.7 19.0 - - + +
247A LYS* 3.2 45.3 + - + +
248A PHE 3.2 1.0 - - - -
249A GLU* 1.3 78.1 - - + +
251A ILE* 1.3 62.0 + - - +
253A GLY* 3.8 1.5 + - - -
254A VAL* 3.5 23.2 + - - +
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Residues in contact with ILE 251 (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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202A CYS* 5.5 2.9 - - + -
205A PRO* 4.5 8.1 - - + +
208A PHE* 3.7 36.1 - - + -
237A GLY 5.3 2.5 - - - +
238A PHE* 4.3 11.4 - - + -
239A PRO* 3.9 28.3 - - + -
246A LEU* 3.6 33.9 - - + +
247A LYS 3.3 11.7 - - - +
248A PHE* 3.0 7.0 + - - +
250A GLU* 1.3 76.4 - - - +
252A THR* 1.3 60.7 + - + +
254A VAL* 3.0 8.5 + - - +
255A ILE* 2.9 38.4 + - + +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 3.9 14.9 + - + +
59A LEU* 3.6 28.0 - - + -
238A PHE* 5.2 0.4 - - + -
248A PHE* 2.9 46.0 + - + +
249A GLU* 3.1 18.2 + - - +
251A ILE* 1.3 77.3 - - + +
253A GLY* 1.3 58.9 + - - +
254A VAL 3.0 0.4 - - - -
255A ILE* 3.9 11.2 - - + -
256A ASN* 2.9 38.0 + - - -
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Residues in contact with GLY 253 (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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249A GLU 2.9 18.4 + - - -
250A GLU 4.2 2.2 - - - -
251A ILE 3.2 0.6 - - - -
252A THR* 1.3 77.2 + - - +
254A VAL* 1.3 60.6 + - - +
256A ASN* 4.9 3.1 - - - -
257A PRO* 3.2 19.0 - - - +
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Residues in contact with VAL 254 (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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205A PRO* 4.0 33.0 - - + +
206A GLU* 4.9 2.0 - - - +
208A PHE* 5.8 0.2 - - + -
209A VAL* 3.6 25.9 - - + +
250A GLU 3.5 16.2 - - - +
251A ILE 3.0 7.3 + - - +
253A GLY* 1.3 80.7 - - - +
255A ILE* 1.3 64.7 + - + +
256A ASN 3.5 0.4 - - - -
257A PRO* 3.2 16.9 - - + +
258A ALA* 3.5 10.4 + - - +
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Residues in contact with ILE 255 (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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59A LEU* 4.0 12.1 - - + -
208A PHE* 3.7 33.0 - - + -
212A ILE* 4.5 7.0 - - + -
234A ILE* 4.2 15.3 - - + -
238A PHE* 3.6 30.5 - - + -
251A ILE* 2.9 25.8 + - + +
252A THR* 3.1 11.6 + - - +
254A VAL* 1.3 76.5 - - + +
256A ASN* 1.3 58.4 + - - +
258A ALA* 3.0 9.7 + - - +
259A LEU* 2.9 49.9 + - + +
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Residues in contact with ASN 256 (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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58A ALA 2.8 25.8 + - - +
59A LEU* 3.4 22.0 - - - +
60A PRO* 4.5 7.2 - - - +
61A ARG* 5.6 5.4 + - - +
62A VAL* 5.3 0.7 - - - +
252A THR* 2.9 22.6 + - - +
253A GLY* 4.9 2.3 - - - -
255A ILE* 1.3 77.6 - - - +
257A PRO* 1.3 68.1 - - + +
259A LEU* 3.3 13.5 + - - +
260A ASP* 3.0 32.5 + - - +
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Residues in contact with PRO 257 (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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253A GLY 3.2 24.5 - - - +
254A VAL* 3.2 19.3 - - + +
256A ASN* 1.3 93.8 - - + +
258A ALA* 1.3 60.1 + - - +
260A ASP* 3.4 9.5 + - + +
261A LYS* 3.1 24.3 + - - +
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Residues in contact with ALA 258 (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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209A VAL* 4.0 28.9 - - + -
212A ILE* 3.8 19.4 - - + +
254A VAL 3.6 9.9 - - - +
255A ILE* 3.0 9.8 + - - +
257A PRO* 1.3 81.4 - - - +
259A LEU* 1.3 62.0 + - - +
261A LYS* 3.4 2.4 + - - -
262A TYR* 3.1 39.9 + - + +
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Residues in contact with LEU 259 (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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61A ARG* 3.6 18.6 - - + +
62A VAL* 4.0 25.4 - - + -
212A ILE* 3.7 22.4 - - + -
232A LEU* 3.9 25.6 - - + -
234A ILE* 4.5 8.5 - - + -
255A ILE* 2.9 34.8 + - + +
256A ASN* 3.6 17.5 - - - +
257A PRO 3.3 0.2 - - - -
258A ALA* 1.3 77.8 - - - +
260A ASP* 1.3 55.5 + - - +
263A PHE* 2.6 39.5 + - + +
271A ILE* 4.0 13.9 - - + -
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Residues in contact with ASP 260 (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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61A ARG* 3.1 28.5 + - - +
256A ASN* 3.0 26.1 + - - +
257A PRO* 3.7 8.9 - - + +
258A ALA 3.4 0.2 - - - -
259A LEU* 1.3 76.0 - - - +
261A LYS* 1.3 61.3 + - - +
263A PHE 4.4 0.7 - - - -
264A PRO* 3.6 22.3 - - - +
265A SER* 5.0 1.9 + - - -
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Residues in contact with LYS 261 (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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216A ARG* 4.2 5.0 + - - -
257A PRO 3.1 17.5 + - - +
258A ALA* 3.8 4.3 - - - +
259A LEU 3.2 0.2 - - - -
260A ASP* 1.3 79.6 - - - +
262A TYR* 1.3 104.4 + - + +
264A PRO* 4.1 6.4 - - - +
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Residues in contact with TYR 262 (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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209A VAL* 4.4 21.2 - - + +
212A ILE* 3.9 14.1 - - + -
213A SER* 4.0 34.5 - - - -
216A ARG* 2.8 52.1 + - + +
258A ALA* 3.1 27.9 + - + +
261A LYS* 1.3 122.7 + - + +
263A PHE* 1.3 77.1 + - + +
264A PRO* 3.7 2.0 - - - +
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Residues in contact with PHE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 2.5 31.7 + - - -
212A ILE* 3.6 34.1 - - + -
215A ALA* 3.9 10.8 - - + -
216A ARG* 3.5 30.3 - - + -
219A PHE* 3.7 34.1 - + - -
232A LEU* 3.5 25.1 - - + -
259A LEU* 2.6 23.2 + - + +
262A TYR* 1.3 83.6 - - + +
264A PRO* 1.3 57.8 - - - +
267A SER* 4.6 1.6 - - - -
269A VAL* 3.8 29.6 - - + -
271A ILE* 4.6 7.9 - - + -
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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