Contacts of the helix formed by residues 290 - 299 (chain A) in PDB entry 4J6I
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 PHE 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO* 4.3 1.8 - - + -
201A TRP 3.6 8.5 - - - +
202A VAL* 3.7 17.5 - - + -
241A PRO* 3.7 23.1 - - + -
280A TYR 4.0 6.3 - - - -
281A LEU* 3.6 25.6 - - + -
282A VAL 3.3 37.7 - - - -
285A THR* 3.4 33.7 - - - -
286A PRO 3.5 9.6 - - - -
287A ILE* 3.3 21.2 + - + +
288A LYS 3.3 2.4 - - - -
289A ASN* 1.3 79.9 - - - +
291A GLN* 1.3 64.9 + - - +
292A TRP* 4.4 2.0 - - + +
293A VAL* 3.0 22.2 + - + +
294A ARG* 3.3 13.5 + - - +
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Residues in contact with GLN 291 (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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201A TRP* 3.0 62.6 + - + +
203A THR* 3.5 30.4 + - + +
289A ASN 4.0 1.6 + - - -
290A PHE* 1.3 70.8 - - - +
292A TRP* 1.3 63.1 + - - +
294A ARG* 3.1 19.5 + - - +
295A HIS* 2.9 24.3 + - - +
654A ASP* 4.0 13.6 + - - +
856A GLU* 5.0 9.7 + - - -
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Residues in contact with TRP 292 (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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201A TRP* 4.7 9.5 + + + +
274A VAL* 3.2 48.8 - - + +
275A CYS 5.4 1.3 - - - -
277A ARG* 3.5 35.7 - - - -
279A GLU* 4.5 22.2 - - + -
281A LEU* 4.5 14.8 - - + -
290A PHE* 3.2 1.2 - - - +
291A GLN* 1.3 78.9 - - - +
293A VAL* 1.3 63.6 + - + +
295A HIS* 3.3 34.6 + + + +
296A CYS* 3.2 43.5 + - - -
301A GLU* 5.8 2.5 - - - -
303A ILE* 5.0 10.7 - - + +
304A HIS 4.8 5.3 + - - +
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Residues in contact with VAL 293 (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 ILE* 4.4 16.8 - - + -
222A ILE* 5.4 3.8 - - + -
281A LEU* 4.5 20.9 - - + -
287A ILE* 3.3 35.4 - - + +
288A LYS* 4.8 2.9 - - - -
290A PHE* 3.0 15.2 + - + +
292A TRP* 1.3 77.8 - - + +
294A ARG* 1.3 57.8 + - + +
296A CYS* 3.1 8.3 + - - +
297A LEU* 3.0 46.9 + - + +
303A ILE* 4.6 21.8 - - + -
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Residues in contact with ARG 294 (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 THR* 3.6 29.9 + - - +
205A LYS* 2.7 32.1 + - - +
206A PRO 3.9 10.1 + - - -
207A LEU* 3.6 36.1 - - + +
208A PRO* 4.2 1.7 - - - +
211A LEU* 3.9 18.9 - - + +
288A LYS* 2.6 19.9 + - - +
289A ASN* 3.0 22.4 + - - +
290A PHE 3.6 10.1 - - - +
291A GLN* 3.1 22.2 + - - +
293A VAL* 1.3 73.2 - - + +
295A HIS* 1.3 64.2 + - - +
297A LEU* 3.7 9.8 + - + -
298A LYS* 3.4 18.4 + - - +
856A GLU* 4.0 16.0 + - - -
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Residues in contact with HIS 295 (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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291A GLN* 2.9 14.0 + - - +
292A TRP* 3.3 45.3 - + + +
294A ARG* 1.3 74.9 - - - +
296A CYS* 1.3 69.9 + - - +
298A LYS* 3.5 10.0 + - - +
299A ASN* 3.4 39.4 + - - +
301A GLU* 2.9 22.3 + - - -
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Residues in contact with CYS 296 (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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214A LYS* 3.6 0.2 + - - -
292A TRP* 3.2 44.0 - - - -
293A VAL 3.1 7.8 + - - +
295A HIS* 1.3 82.7 - - - +
297A LEU* 1.3 65.7 + - - +
299A ASN 3.6 0.2 + - - -
300A GLY 3.2 3.6 + - - -
301A GLU* 2.9 53.1 + - - +
302A GLU 4.4 11.0 - - - -
303A ILE* 3.9 24.7 - - + -
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Residues in contact with LEU 297 (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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207A LEU* 4.4 20.0 - - + -
211A LEU* 4.0 15.2 - - + +
214A LYS* 2.9 49.5 + - + +
215A ILE* 4.6 17.3 - - + -
220A ILE* 4.3 28.5 - - + -
288A LYS* 6.3 1.1 - - - -
293A VAL* 3.0 27.6 + - + +
294A ARG* 3.9 14.4 - - + +
296A CYS* 1.3 76.1 - - - +
298A LYS* 1.3 62.2 + - - +
301A GLU 6.0 0.2 - - - +
303A ILE* 4.5 13.9 - - + -
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Residues in contact with LYS 298 (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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210A TYR* 6.0 2.9 - - + -
211A LEU* 3.6 21.0 - - + +
214A LYS* 5.2 1.2 - - - +
294A ARG 3.4 8.6 + - - +
295A HIS* 3.8 8.7 - - - +
296A CYS 3.3 0.8 - - - -
297A LEU* 1.3 79.3 - - - +
299A ASN* 1.3 73.6 + - - +
300A GLY 3.1 4.1 + - - -
852A GLU* 4.8 4.4 + - - -
861A ASP* 3.2 36.7 + - - +
863A CYS* 4.0 15.1 - - - +
864A LEU 4.6 6.7 + - - -
865A LEU* 5.7 3.2 - - - +
927A ARG* 3.3 31.4 + - - +
959A ASN* 5.3 2.2 - - - +
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Residues in contact with ASN 299 (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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295A HIS* 3.4 39.2 + - - +
298A LYS* 1.3 94.6 + - - +
300A GLY* 1.3 62.2 + - - +
301A GLU* 3.2 25.2 + - + +
927A ARG* 3.5 22.6 + - - +
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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