Contacts of the helix formed by residues 287 - 301 (chain P) in PDB entry 3H1J
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 ASN 287 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E ARG* 5.4 1.1 - - - +
141E HIS* 5.1 0.5 + - - -
175E PRO* 3.9 9.7 - - - +
285P ILE* 2.9 18.9 + - + +
286P PRO* 1.3 80.4 - - + +
288P LYS* 1.3 68.1 + - - +
289P LEU* 2.7 11.9 + - - +
290P GLY* 2.5 31.9 + - - -
291P GLY* 3.1 17.0 + - - -
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Residues in contact with LYS 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E THR 3.4 9.9 + - - -
141E HIS* 2.9 48.2 + - + +
142E LEU* 4.2 5.8 - - + -
175E PRO 3.3 17.5 + - - +
177E PRO* 4.1 26.6 - - + +
3103E UNL 4.3 4.6 + - - -
152P SER* 3.2 31.1 + - - -
153P ALA* 4.5 17.0 - - + +
159P HIS* 5.4 4.0 + - - -
282P LEU* 5.9 0.2 - - - +
287P ASN* 1.3 78.0 + - - +
289P LEU* 1.3 64.8 - - - +
291P GLY* 3.8 0.7 - - - -
292P VAL* 3.1 25.8 + - + +
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Residues in contact with LEU 289 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P ALA* 3.8 32.5 - - + +
155P PRO* 5.8 6.7 - - + -
287P ASN* 2.7 11.5 + - - +
288P LYS* 1.3 75.2 - - - +
290P GLY* 1.3 64.7 + - - +
292P VAL* 3.2 6.2 + - + +
293P LEU* 2.9 56.3 + - + +
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Residues in contact with GLY 290 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285P ILE* 3.8 17.7 - - - -
287P ASN* 2.5 20.5 + - - -
289P LEU* 1.3 72.5 - - - +
291P GLY* 1.3 52.4 + - - +
293P LEU* 3.0 12.8 + - - +
294P ALA* 2.7 35.5 + - - +
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Residues in contact with GLY 291 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282P LEU* 3.5 35.6 - - - +
285P ILE* 3.4 12.6 - - - +
287P ASN 3.1 16.1 + - - -
288P LYS 3.8 0.9 - - - -
290P GLY* 1.3 74.8 - - - +
292P VAL* 1.3 56.2 + - - +
294P ALA* 3.4 5.2 + - - +
295P LEU* 2.8 28.4 + - - +
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Residues in contact with VAL 292 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E HIS* 5.9 1.3 - - - +
142E LEU* 5.5 4.0 - - + -
150P LEU* 4.0 33.9 - - + +
153P ALA* 3.6 31.2 - - + -
282P LEU* 4.3 4.5 - - + +
288P LYS* 3.1 19.2 + - + +
289P LEU* 3.6 9.0 - - + +
290P GLY 3.1 0.4 - - - -
291P GLY* 1.3 72.4 - - - +
293P LEU* 1.3 57.1 + - + +
295P LEU* 2.8 11.2 + - + +
296P ALA* 2.7 36.6 + - + +
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Residues in contact with LEU 293 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289P LEU* 2.9 52.7 + - + +
290P GLY* 3.4 9.6 - - - +
292P VAL* 1.3 76.5 - - + +
294P ALA* 1.3 53.4 + - - +
296P ALA* 3.3 9.4 + - + +
297P ALA* 2.7 36.7 + - - +
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Residues in contact with ALA 294 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281P ILE* 3.9 16.2 - - + +
285P ILE* 3.6 28.0 - - + -
290P GLY 2.7 20.5 + - - +
291P GLY 3.5 4.9 - - - +
293P LEU* 1.3 72.2 - - - +
295P LEU* 1.3 55.2 + - - +
297P ALA* 3.1 6.7 + - - +
298P SER* 2.6 36.6 + - - -
360P PHE* 3.7 8.5 - - + -
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Residues in contact with LEU 295 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150P LEU* 3.9 21.8 - - + -
278P ALA* 3.4 38.1 - - + +
281P ILE* 4.7 2.9 - - - +
282P LEU* 3.5 27.6 - - + -
291P GLY 2.8 13.9 + - - +
292P VAL* 2.8 12.1 + - + +
294P ALA* 1.3 74.9 - - - +
296P ALA* 1.3 64.7 + - - +
298P SER* 2.4 25.6 + - - +
299P VAL* 3.6 4.0 + - + +
3001P SMA 3.5 43.8 - - + +
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Residues in contact with ALA 296 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292P VAL* 2.7 19.4 + - + +
293P LEU* 3.5 13.7 - - + +
295P LEU* 1.3 73.3 - - - +
297P ALA* 1.3 53.3 + - - +
299P VAL* 3.1 6.0 + - - +
300P LEU* 2.8 52.8 + - + +
3001P SMA 5.6 4.0 - - - -
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Residues in contact with ALA 297 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293P LEU 2.7 22.5 + - - +
294P ALA* 3.4 6.3 - - - +
296P ALA* 1.3 68.1 - - - +
298P SER* 1.3 64.0 + - - +
299P VAL 2.9 6.7 + - - -
300P LEU* 4.4 6.7 - - - +
301P ILE* 2.9 29.9 + - + +
360P PHE* 3.8 15.7 - - + -
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Residues in contact with SER 298 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277P PHE* 4.6 8.0 - - - -
278P ALA* 4.1 4.4 - - - +
281P ILE* 3.7 29.8 - - - -
294P ALA 2.6 16.4 + - - -
295P LEU* 2.4 32.7 + - - +
297P ALA* 1.3 72.4 - - - +
299P VAL* 1.3 66.4 + - - +
301P ILE* 3.7 3.4 - - - +
302P LEU* 5.5 0.3 - - - +
359P TYR* 2.9 25.2 + - - -
360P PHE* 3.6 11.8 - - - -
3007P PEE 4.8 2.9 - - - +
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Residues in contact with VAL 299 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P VAL* 4.6 3.8 - - + +
121P LEU* 4.1 21.3 - - + -
122P LEU* 3.6 32.5 - - + -
125P MET* 4.0 24.5 - - + -
277P PHE* 4.5 11.2 - - + -
278P ALA* 5.2 2.2 - - + -
295P LEU 4.4 2.7 - - - +
296P ALA* 3.1 5.8 + - - +
297P ALA 3.0 0.2 - - - -
298P SER* 1.3 91.6 + - - +
300P LEU* 1.3 67.3 + - + +
301P ILE 3.0 2.8 + - - -
302P LEU* 3.1 26.3 + - + +
3001P SMA 4.5 11.0 - - - -
3007P PEE 5.4 2.7 - - + -
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Residues in contact with LEU 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P VAL* 5.4 0.2 - - - -
122P LEU* 3.9 22.0 - - + -
296P ALA* 2.8 33.4 + - + +
297P ALA* 4.4 4.3 - - - +
299P VAL* 1.3 77.9 - - + +
301P ILE* 1.3 62.3 + - - +
302P LEU 3.0 0.4 - - - -
303P PHE* 2.9 53.6 + - + +
304P LEU* 5.4 0.7 - - - +
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Residues in contact with ILE 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P ALA* 2.9 22.5 + - + +
298P SER* 3.7 16.4 - - - +
299P VAL 4.2 0.7 - - - +
300P LEU* 1.3 77.2 - - - +
302P LEU* 1.3 60.6 + - + +
304P LEU* 2.8 37.3 + - + +
305P ILE* 3.5 8.0 + - + +
308P LEU* 6.0 0.7 - - + -
359P TYR* 3.9 12.3 - - + +
360P PHE* 4.1 17.0 - - + -
363P LEU* 3.8 32.3 - - + -
364P LEU* 3.6 36.6 - - + -
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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