Contacts of the helix formed by residues 302 - 317 (chain A) in PDB entry 3HOT
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A PHE* 3.9 4.5 - - - -
189A LYS* 6.1 0.2 - - - +
300A PHE* 4.0 0.7 - - - +
301A ASP* 1.3 89.9 + - - +
303A TYR* 1.3 64.5 + - - +
304A GLU* 3.4 19.3 - - - +
305A SER* 2.9 35.9 + - - -
306A VAL* 3.3 8.0 + - - +
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Residues in contact with TYR 303 (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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162A PHE* 3.8 20.7 - - + -
189A LYS* 5.9 0.6 - - - +
191A THR* 3.6 18.4 - - + -
207A LEU* 3.2 46.4 + - + +
209A LYS* 3.8 26.3 - - + +
210A PRO* 3.8 15.7 - - + -
302A SER* 1.3 72.6 - - - +
304A GLU* 1.3 82.6 + - + +
306A VAL* 3.1 24.4 - - - +
307A LYS* 3.3 24.5 + - + -
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Residues in contact with GLU 304 (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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302A SER* 3.4 18.9 - - - +
303A TYR* 1.3 99.8 + - + +
305A SER* 1.3 55.2 + - - +
306A VAL 3.1 1.3 - - - -
307A LYS* 2.9 9.8 + - + +
308A LYS* 2.7 36.0 + - - +
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Residues in contact with SER 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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300A PHE* 3.5 21.9 - - - -
301A ASP* 4.4 6.3 + - - -
302A SER* 2.9 29.7 + - - -
304A GLU* 1.3 74.7 - - - +
306A VAL* 1.3 55.6 + - - +
308A LYS* 3.5 7.9 + - - +
309A TRP* 3.0 29.3 + - - +
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Residues in contact with VAL 306 (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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160A ILE* 4.1 18.8 - - + -
162A PHE* 4.3 14.8 - - + -
191A THR* 4.0 13.7 - - - +
207A LEU* 3.7 19.7 - - + -
300A PHE* 3.5 33.2 - - + -
302A SER 3.8 7.4 - - - +
303A TYR* 3.1 19.7 - - - +
304A GLU 3.1 0.2 - - - -
305A SER* 1.3 78.0 - - - +
307A LYS* 1.3 53.5 + - - +
309A TRP* 3.2 2.1 + - - +
310A LEU* 2.8 41.7 + - + +
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Residues in contact with LYS 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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205A TYR* 3.4 31.9 + - + +
206A GLU* 6.2 0.4 - - - +
207A LEU* 4.4 14.7 - - + +
303A TYR* 3.3 27.3 + - + +
304A GLU* 2.9 18.4 + - + +
306A VAL* 1.3 77.7 - - - +
308A LYS* 1.3 60.3 + - - +
310A LEU* 4.5 4.3 - - - -
311A ASP* 2.8 53.5 + - - +
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Residues in contact with LYS 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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304A GLU 2.7 17.8 + - - +
305A SER* 3.9 7.9 - - - +
307A LYS* 1.3 73.1 - - - +
309A TRP* 1.3 57.1 + - - +
311A ASP* 3.9 5.1 - - - +
312A GLU* 2.9 57.2 + - + +
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Residues in contact with TRP 309 (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 MET* 4.3 2.9 - - + -
294A ALA* 3.2 49.1 - - + -
295A LEU* 3.7 22.2 - - + -
298A GLN* 2.5 25.8 + - - -
300A PHE* 3.6 23.3 - + + -
305A SER 3.0 18.8 + - - +
306A VAL 3.4 4.5 - - - +
307A LYS 3.1 0.2 - - - -
308A LYS* 1.3 74.4 - - - +
310A LEU* 1.3 73.3 + - + +
312A GLU* 3.3 3.9 + - - +
313A TRP* 2.8 65.7 + + + +
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Residues in contact with LEU 310 (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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160A ILE* 3.6 23.3 - - + -
193A LEU* 3.7 37.9 - - + -
205A TYR* 3.9 17.5 - - + +
207A LEU* 4.2 9.4 - - + -
291A MET* 4.5 6.3 - - - -
300A PHE* 6.0 0.2 - - + -
306A VAL* 2.8 35.7 + - + +
307A LYS* 3.8 3.1 - - - +
309A TRP* 1.3 91.9 - - + +
311A ASP* 1.3 64.6 + - - +
313A TRP* 2.9 14.0 + - + +
314A PHE* 3.0 34.0 + - + -
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Residues in contact with ASP 311 (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 TYR* 2.7 29.8 + - - -
307A LYS* 2.8 40.9 + - - +
308A LYS* 3.9 5.3 + - - +
310A LEU* 1.3 71.4 - - - +
312A GLU* 1.3 64.4 + - + +
314A PHE* 3.6 6.0 + - - +
315A ALA* 3.1 25.7 + - - +
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Residues in contact with GLU 312 (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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308A LYS* 2.9 46.7 + - + +
309A TRP* 3.9 3.6 - - - +
311A ASP* 1.3 78.1 - - + +
313A TRP* 1.3 57.5 + - - +
315A ALA* 3.9 6.1 - - + +
316A ALA* 2.9 33.1 + - - +
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Residues in contact with TRP 313 (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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287A LEU* 3.7 33.4 - - + -
290A SER* 3.5 14.8 - - - -
291A MET* 3.6 47.6 - - + -
294A ALA* 3.7 17.2 - - + +
309A TRP* 2.8 48.1 + + + +
310A LEU* 2.9 5.1 + - + +
312A GLU* 1.3 74.5 - - - +
314A PHE* 1.3 85.1 + + - +
316A ALA* 3.3 5.5 + - + +
317A LYS* 2.9 62.5 + - + +
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Residues in contact with PHE 314 (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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193A LEU* 4.7 8.7 - - + -
195A VAL* 4.2 26.9 - - + -
202A VAL* 3.8 27.5 - - + +
205A TYR* 4.3 27.6 - + - -
287A LEU* 4.3 13.5 - - + -
291A MET* 5.4 1.6 - - - -
310A LEU* 3.0 46.9 + - + +
311A ASP* 4.1 4.3 - - - +
313A TRP* 1.3 102.0 - + - +
315A ALA* 1.3 62.2 + - - +
317A LYS* 3.3 18.1 + - - +
318A ASP 5.3 0.2 - - - +
322A TYR* 3.4 23.5 + + - -
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Residues in contact with ALA 315 (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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311A ASP 3.1 16.8 + - - +
312A GLU* 3.9 6.7 - - - +
314A PHE* 1.3 80.6 - - - +
316A ALA* 1.3 60.4 + - - +
317A LYS 3.5 7.6 - - - +
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Residues in contact with ALA 316 (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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312A GLU 2.9 19.1 + - - +
313A TRP* 3.6 4.7 - - + +
315A ALA* 1.3 73.3 - - - +
317A LYS* 1.3 64.5 + - - +
318A ASP* 3.7 0.7 + - - -
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Residues in contact with LYS 317 (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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290A SER* 3.4 16.9 + - - -
313A TRP* 2.9 54.9 + - + +
314A PHE* 3.4 16.2 - - - +
315A ALA 3.2 10.5 - - - +
316A ALA* 1.3 81.4 - - - +
318A ASP* 1.3 71.2 + - + +
319A ASP* 5.5 0.3 - - - +
321A PHE* 3.7 37.7 - - + -
322A TYR* 3.6 19.7 - - + +
5E G 4.4 6.3 + - - -
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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