Contacts of the helix formed by residues 244 - 255 (chain A) in PDB entry 3A7H
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 SER 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLU* 2.5 36.4 + - - -
243A TYR* 1.3 76.0 - - - +
245A LYS* 1.3 68.5 + - - +
246A PRO* 3.6 11.2 - - - +
247A LEU* 3.2 14.7 + - - +
248A LYS* 3.1 19.6 + - - +
273A PHE* 4.2 3.8 - - - -
277A ASN* 4.9 2.5 + - - -
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Residues in contact with LYS 245 (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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243A TYR 3.7 1.4 + - - -
244A SER* 1.3 71.4 - - - +
246A PRO* 1.3 67.7 - - + +
248A LYS* 3.2 10.8 + - + +
249A GLU* 2.9 60.7 + - + +
272A LYS* 4.5 11.3 - - - +
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Residues in contact with PRO 246 (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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244A SER* 3.4 15.3 - - - +
245A LYS* 1.3 96.3 - - + +
247A LEU* 1.3 56.1 + - - +
249A GLU* 3.2 5.6 + - + -
250A PHE* 2.8 30.5 + - - +
271A HIS* 3.3 6.9 - - + -
272A LYS* 3.6 31.9 - - + +
273A PHE* 3.8 29.8 - - + +
276A ARG* 3.7 17.0 - - - +
277A ASN* 5.3 1.8 - - - +
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Residues in contact with LEU 247 (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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118A GLU* 3.9 23.1 - - + +
121A ILE* 4.2 19.3 - - + -
125A LEU* 4.8 6.1 - - + -
209A ALA* 4.9 4.7 - - + +
213A ALA* 4.5 2.5 - - + -
239A LEU* 3.4 24.7 - - + -
243A TYR* 3.9 13.5 - - + -
244A SER* 3.2 16.7 + - - +
246A PRO* 1.3 76.5 - - - +
248A LYS* 1.3 64.3 + - - +
250A PHE* 3.2 4.9 + - + +
251A VAL* 3.0 29.4 + - + +
273A PHE* 3.5 44.4 - - + -
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Residues in contact with LYS 248 (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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239A LEU* 3.5 42.4 + - + +
240A GLU* 4.8 0.6 - - - +
241A GLY 2.9 34.1 + - - +
243A TYR* 3.7 20.0 + - + +
244A SER 3.1 12.4 + - - +
245A LYS* 3.6 9.9 - - - +
247A LEU* 1.3 76.2 - - - +
249A GLU* 1.3 60.5 + - + +
251A VAL* 3.4 3.1 + - - +
252A GLU* 3.0 29.6 + - + +
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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
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245A LYS* 2.9 55.8 + - + +
246A PRO 3.8 4.0 - - - +
248A LYS* 1.3 75.3 - - + +
250A PHE* 1.3 61.1 + - - +
252A GLU* 3.2 20.9 + - - +
253A ALA* 2.8 30.5 + - - +
271A HIS* 3.8 12.8 + - + +
272A LYS* 3.9 18.4 - - - -
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Residues in contact with PHE 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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125A LEU* 4.0 24.0 - - + -
129A LEU* 4.0 19.1 - - + -
205A LEU* 4.1 16.2 - - + -
209A ALA* 4.2 15.9 - - + -
246A PRO 2.8 18.1 + - - +
247A LEU* 3.4 7.9 - - + +
249A GLU* 1.3 76.3 - - - +
251A VAL* 1.3 66.4 + - + +
253A ALA* 3.3 3.9 + - - +
254A CYS* 3.2 35.0 + - - -
268A LEU* 3.8 20.4 - - + -
271A HIS* 3.6 32.5 - + + +
273A PHE* 4.1 12.8 - + + -
274A ILE* 3.7 27.4 - - + -
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Residues in contact with VAL 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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206A GLY* 4.3 3.4 - - - +
209A ALA* 3.9 24.9 - - + -
210A ILE* 3.7 25.1 - - + +
237A PRO 4.6 0.9 - - - +
238A THR* 4.6 4.0 - - - -
239A LEU* 4.2 28.0 - - + +
247A LEU* 3.0 20.5 + - + +
248A LYS 3.7 7.6 - - - +
250A PHE* 1.3 79.9 - - - +
252A GLU* 1.3 56.8 + - - +
254A CYS* 3.4 4.4 + - - +
255A LEU* 2.9 51.5 + - + +
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Residues in contact with GLU 252 (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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237A PRO 5.6 2.2 - - - -
238A THR* 5.0 20.4 - - + +
248A LYS* 3.0 16.5 + - + +
249A GLU* 3.2 26.9 + - - +
251A VAL* 1.3 77.8 - - - +
253A ALA* 1.3 65.4 + - - +
255A LEU* 3.3 21.3 + - - +
256A ASN* 4.0 3.6 + - - +
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Residues in contact with ALA 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 2.8 16.5 + - - +
250A PHE* 3.3 9.2 + - - +
252A GLU* 1.3 79.1 - - - +
254A CYS* 1.3 61.8 + - - +
256A ASN* 4.3 7.4 + - - +
261A PHE 4.7 1.0 - - - +
262A ARG* 4.1 5.2 - - - +
263A PRO* 3.5 24.9 - - + +
268A LEU* 4.5 15.0 - - + -
271A HIS* 4.7 7.9 - - + +
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Residues in contact with CYS 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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202A ILE* 3.3 29.4 - - - +
203A TRP* 3.7 6.6 - - - -
205A LEU* 4.3 2.9 - - - -
206A GLY* 3.5 20.4 - - - -
250A PHE* 3.2 37.6 + - - -
251A VAL 3.8 2.7 - - - +
253A ALA* 1.3 76.1 - - - +
255A LEU* 1.3 59.6 + - - +
256A ASN 3.2 0.3 + - - -
262A ARG* 3.2 28.2 + - - -
268A LEU* 3.9 24.2 - - - -
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Residues in contact with LEU 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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203A TRP* 3.3 60.1 - - + +
206A GLY* 3.9 7.9 - - - -
207A ILE* 3.8 19.3 - - + +
210A ILE* 3.6 18.8 - - + -
236A PRO* 2.9 25.9 - - + +
237A PRO* 3.7 21.1 - - + +
251A VAL* 2.9 38.6 + - + +
252A GLU* 3.3 10.3 + - - +
254A CYS* 1.3 75.5 - - - +
256A ASN* 1.3 57.8 + - - +
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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