Contacts of the helix formed by residues 299 - 309 (chain A) in PDB entry 4II9
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 ASP 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ILE* 3.6 2.4 - - - +
293A GLU* 2.7 38.6 + - + +
294A SER* 2.8 35.7 + - - +
296A SER* 3.0 7.1 + - - +
297A THR 3.2 0.2 - - - -
298A ASP* 1.4 76.2 - - - +
300A SER* 1.3 61.1 + - - +
301A LEU* 2.9 23.3 + - - +
302A TYR* 3.1 10.7 + - + +
303A VAL* 3.0 28.7 + - - +
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A THR 5.5 0.2 - - - -
298A ASP 3.7 4.8 + - - -
299A ASP* 1.3 74.3 + - - +
301A LEU* 1.3 65.6 + - - +
303A VAL* 3.8 9.1 - - - +
304A PHE* 3.3 23.0 + - - +
8C C 3.3 41.0 + - - -
9C C 3.6 17.5 + - - +
10C A9Z 5.3 5.4 + - - -
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Residues in contact with LEU 301 (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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138A MET* 4.0 27.4 - - + -
291A GLY 3.8 22.4 - - - +
292A ILE* 3.9 6.3 - - + -
293A GLU* 4.6 1.8 - - + +
299A ASP* 2.9 13.8 + - - +
300A SER* 1.3 78.2 + - - +
302A TYR* 1.3 65.5 + - - +
304A PHE* 3.5 3.2 + - - +
305A LYS* 3.1 31.7 + - - +
9C C 6.2 2.9 - - - -
10C A9Z 3.5 73.6 - - + +
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Residues in contact with TYR 302 (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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148A MET* 3.5 30.5 - - + -
292A ILE* 3.7 24.4 - - + +
294A SER 3.4 19.3 - - - +
295A GLU* 3.8 29.2 + - + +
296A SER* 3.2 28.9 - - - +
297A THR* 4.4 11.9 - - + -
299A ASP* 3.1 10.3 + - + +
301A LEU* 1.3 82.3 - - - +
303A VAL* 1.3 62.5 + - + +
305A LYS* 4.5 1.1 - - - +
306A HIS* 2.8 67.2 + + + +
313A PRO* 4.7 3.1 - - + -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER 4.3 0.2 - - - +
297A THR* 3.4 42.0 - - + +
299A ASP 3.0 13.5 + - - +
300A SER* 3.9 9.0 - - - +
301A LEU 3.4 0.2 - - - -
302A TYR* 1.3 79.2 - - + +
304A PHE* 1.3 65.4 + - - +
306A HIS* 3.6 7.1 + - - +
307A VAL* 3.6 14.7 + - + +
8C C 5.1 9.0 - - - +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 4.5 16.4 - + - -
268A PRO* 3.8 24.2 - - + -
269A TYR* 3.3 38.6 - + - -
272A GLN* 3.8 39.5 - - + -
289A LEU* 4.9 1.1 - - + -
300A SER 3.3 15.0 + - - +
301A LEU* 4.0 3.1 - - - +
302A TYR 3.2 0.2 - - - -
303A VAL* 1.3 78.4 - - - +
305A LYS* 1.3 80.0 + - + +
307A VAL* 3.1 27.2 + - - +
308A PHE* 3.9 8.2 - + - -
8C C 5.4 2.0 + - - +
9C C 3.9 29.6 - - - +
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Residues in contact with LYS 305 (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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148A MET* 3.6 22.2 - - + -
254A TYR* 4.5 6.5 - - - -
289A LEU* 2.7 52.3 + - + +
290A GLY 3.4 10.6 - - - +
291A GLY 2.7 28.7 + - - +
292A ILE* 4.0 4.9 - - + -
301A LEU* 3.1 22.5 + - - +
304A PHE* 1.3 86.6 - - + +
306A HIS* 1.3 56.7 + - - +
308A PHE* 3.0 20.1 + - - +
309A VAL* 3.0 14.0 + - - +
10C A9Z 2.8 32.3 + - - -
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Residues in contact with HIS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.4 7.5 - - + +
302A TYR* 2.8 55.2 + + + +
303A VAL* 4.0 4.9 - - - +
304A PHE 3.3 0.2 - - - -
305A LYS* 1.3 73.6 - - - +
307A VAL* 1.3 58.2 + - - +
308A PHE 3.1 0.6 + - - -
309A VAL 3.2 17.6 + - - +
310A LYS* 2.7 73.8 + - + +
311A ASP 4.9 1.9 + - - -
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Residues in contact with VAL 307 (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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165A TYR* 3.8 4.0 - - - -
169A THR* 3.7 26.8 - - + +
172A LYS* 4.3 32.3 - - + +
173A ILE* 5.5 0.9 - - + -
269A TYR* 3.8 26.9 - - + +
303A VAL* 3.6 12.0 + - + +
304A PHE* 3.1 20.0 - - - +
306A HIS* 1.3 79.7 - - - +
308A PHE* 1.3 81.2 + - + +
310A LYS* 3.7 16.3 + - - +
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Residues in contact with PHE 308 (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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150A LEU* 3.9 11.8 - - + +
165A TYR* 2.7 44.2 + + - +
173A ILE* 4.0 24.2 - - + -
269A TYR* 3.8 36.3 - + + -
272A GLN* 3.5 35.9 - - + -
273A SER* 4.6 2.0 - - - -
276A ILE* 3.7 17.0 - - + -
289A LEU* 3.9 24.9 - - + -
304A PHE* 3.9 11.7 - + - -
305A LYS 3.0 5.6 + - - +
307A VAL* 1.3 100.8 - - + +
309A VAL* 1.3 64.1 + - - +
310A LYS 4.1 1.2 + - - -
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.8 27.8 - - + +
149A VAL 3.7 23.1 - - - +
150A LEU* 4.0 15.7 - - + +
289A LEU* 3.5 30.7 - - + -
305A LYS 3.0 9.9 + - - +
306A HIS* 3.2 25.9 + - - +
308A PHE* 1.3 80.5 - - - +
310A LYS* 1.3 59.6 + - - +
311A ASP* 3.6 25.1 - - + +
312A ALA 4.9 1.8 - - - +
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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