Contacts of the helix formed by residues 299 - 319 (chain A) in PDB entry 1H13
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 GLN 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 3.7 25.7 - - - +
296A MET 5.4 0.5 - - - +
297A GLY* 4.3 4.1 - - - +
298A ALA* 1.3 82.0 + - - +
300A ALA* 1.3 68.2 + - - +
301A TRP* 3.1 15.0 - - + +
302A HIS* 3.0 34.3 + - + +
303A LYS* 3.3 19.2 + - - +
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Residues in contact with ALA 300 (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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299A GLN* 1.3 75.9 - - - +
301A TRP* 1.3 63.6 + - - +
303A LYS* 3.3 13.4 + - - +
304A SER* 3.0 25.2 + - - -
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Residues in contact with TRP 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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206A PRO* 5.2 0.7 - - + -
233A ARG* 4.0 26.0 - - + +
236A LEU* 3.8 39.9 - - + -
237A LYS* 3.2 55.8 - - + +
240A PHE* 4.6 5.9 - + + +
289A VAL* 4.1 22.4 - - + -
292A ASP* 4.2 3.4 - - + -
299A GLN* 3.1 16.6 - - + +
300A ALA* 1.3 77.6 - - - +
302A HIS* 1.3 102.7 + + - +
304A SER* 4.0 4.6 - - - -
305A ALA* 3.0 30.0 + - + +
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Residues in contact with HIS 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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233A ARG* 5.1 3.6 - - - -
289A VAL* 3.5 37.9 - - + -
292A ASP* 2.8 27.5 + - + +
293A ALA* 3.8 9.6 - - + -
297A GLY 3.3 20.8 + - - -
298A ALA* 4.7 0.9 - - - -
299A GLN* 3.0 32.4 + - + +
301A TRP* 1.3 111.6 + + - +
303A LYS* 1.3 64.8 + - + +
305A ALA* 3.6 0.9 - - - +
306A VAL* 3.1 29.8 + - - +
354A ALA* 3.8 12.1 - - + -
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Residues in contact with LYS 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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5A ASN* 4.6 10.3 + - - -
6A PRO* 4.2 17.3 + - + +
298A ALA* 4.1 27.3 + - + -
299A GLN 3.5 18.2 - - - +
300A ALA* 3.3 9.7 + - - +
301A TRP 3.2 0.4 - - - -
302A HIS* 1.3 77.0 - - - +
304A SER* 1.3 56.5 + - - +
306A VAL* 3.6 0.3 - - - +
307A ASN* 2.8 40.6 + - - +
354A ALA 3.3 22.0 - - - +
356A THR* 3.7 25.1 - - + +
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Residues in contact with SER 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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300A ALA 3.0 16.2 + - - -
301A TRP* 4.0 5.8 - - - -
303A LYS* 1.3 74.4 - - - +
305A ALA* 1.3 67.7 + - - +
307A ASN* 4.6 4.5 - - - +
308A LYS* 2.9 50.5 + - - +
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Residues in contact with ALA 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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240A PHE* 3.6 51.9 - - + +
250A ASN 4.7 0.5 - - - +
286A ILE* 4.7 0.4 - - - -
289A VAL* 4.5 9.6 - - + -
301A TRP* 3.0 20.8 + - + +
302A HIS* 3.6 4.5 - - - +
304A SER* 1.3 77.6 + - - +
306A VAL* 1.3 59.0 + - + +
308A LYS* 4.3 2.0 - - - +
309A ALA* 3.1 28.8 + - - +
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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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286A ILE* 4.0 22.7 - - + +
289A VAL* 3.7 22.4 - - + -
302A HIS 3.1 15.3 + - - +
303A LYS 3.6 1.3 - - - +
305A ALA* 1.3 73.9 - - - +
307A ASN* 1.3 71.0 + - - +
309A ALA* 4.5 4.0 - - - -
310A LEU* 2.9 31.9 + - + +
351A ALA* 3.8 23.6 - - + +
354A ALA* 3.4 36.3 - - + +
355A SER* 3.6 11.4 - - - +
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Residues in contact with ASN 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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303A LYS* 2.8 36.0 + - - +
304A SER* 4.1 4.2 - - - +
306A VAL* 1.3 72.3 - - - +
308A LYS* 1.3 59.6 + - + +
311A GLY* 2.9 14.6 + - - -
355A SER* 3.4 4.7 + - - -
356A THR* 2.9 45.1 + - - +
357A ASN* 4.2 3.7 + - - -
360A GLN* 2.9 41.0 + - - +
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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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240A PHE 5.6 0.7 - - - -
244A SER* 3.1 30.6 + - - +
245A GLY* 4.6 1.2 - - - +
250A ASN* 3.2 44.3 + - + +
304A SER* 2.9 39.7 + - - +
305A ALA* 4.3 1.3 - - - +
307A ASN* 1.3 76.5 - - + +
309A ALA* 1.3 60.2 + - - +
311A GLY* 3.4 1.6 + - - -
312A PHE* 2.9 22.9 + - - +
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Residues in contact with ALA 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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240A PHE* 5.0 0.2 - - + -
250A ASN 3.4 20.8 + - - +
251A LEU* 3.8 13.7 - - + +
252A PRO* 4.9 1.8 - - + -
286A ILE* 3.9 26.9 - - + -
305A ALA 3.1 20.3 + - - +
306A VAL 3.9 2.2 - - - +
308A LYS* 1.3 75.2 - - - +
310A LEU* 1.3 66.4 + - - +
312A PHE* 3.1 4.3 + - - +
313A LEU* 3.0 27.4 + - - +
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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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286A ILE* 3.7 24.0 - - + -
306A VAL* 2.9 22.4 + - + +
309A ALA* 1.3 74.6 - - - +
311A GLY* 1.3 63.0 + - - +
313A LEU* 3.2 3.5 + - + +
314A SER* 2.9 26.1 + - - -
348A ASN* 3.9 18.6 - - + +
351A ALA* 4.8 6.1 - - + -
352A LEU* 3.6 30.5 - - + -
355A SER* 4.8 3.8 - - - -
360A GLN* 3.8 23.3 - - - +
364A PHE* 3.7 38.9 - - + -
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Residues in contact with GLY 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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307A ASN 2.9 19.8 + - - -
308A LYS* 3.7 2.2 - - - -
309A ALA 3.2 0.4 - - - -
310A LEU* 1.3 77.8 - - - +
312A PHE* 1.3 61.1 + - - +
314A SER* 3.4 6.3 + - - -
315A TYR* 3.0 24.0 + - - +
360A GLN* 3.4 8.0 + - - -
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Residues in contact with PHE 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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249A TRP* 3.4 33.2 - + + +
250A ASN* 4.4 6.7 - - + +
251A LEU* 3.5 34.8 - - + -
308A LYS 2.9 13.7 + - - +
309A ALA 3.1 7.2 + - - +
311A GLY* 1.3 74.6 - - - +
313A LEU* 1.3 62.1 + - + +
315A TYR* 3.1 20.1 + + - +
316A ALA* 2.7 44.2 + - + -
329A TYR* 3.8 18.4 - + - -
332A GLY* 3.4 39.5 - - - -
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Residues in contact with LEU 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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251A LEU* 4.0 29.4 - - + -
278A TYR* 4.0 16.2 - - + +
286A ILE* 5.2 2.2 - - + -
309A ALA 3.0 19.5 + - - +
310A LEU* 3.8 13.9 - - + +
312A PHE* 1.3 81.1 - - + +
314A SER* 1.3 61.8 + - - +
316A ALA* 3.3 2.1 + - - -
317A LYS* 3.0 20.3 + - - +
325A TYR* 3.5 42.5 - - + +
329A TYR* 4.2 10.8 - - + -
348A ASN* 3.4 33.7 - - - +
364A PHE* 4.2 4.5 - - + -
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Residues in contact with SER 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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310A LEU 2.9 16.6 + - - -
311A GLY* 3.7 7.0 - - - -
313A LEU* 1.3 75.3 - - - +
315A TYR* 1.3 63.2 + - - +
317A LYS* 3.3 10.9 + - - +
318A THR* 3.2 26.9 + - - +
325A TYR* 5.5 0.7 - - - -
360A GLN* 6.0 2.9 - - - -
364A PHE* 4.3 14.4 - - - -
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Residues in contact with TYR 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 GLY 3.0 17.9 + - - +
312A PHE* 3.5 20.0 - + - +
314A SER* 1.3 76.4 - - - +
316A ALA* 1.3 66.2 + - - +
318A THR* 2.7 29.5 + - + -
319A ASN* 3.2 29.9 + - + -
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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 PHE* 2.7 35.0 + - + +
313A LEU* 3.6 6.5 - - - +
315A TYR* 1.3 78.1 - - - +
317A LYS* 1.3 62.6 + - - +
319A ASN* 3.1 16.7 + - - +
320A ASN* 3.2 15.2 + - - +
325A TYR* 4.5 0.2 - - + -
329A TYR* 3.4 35.8 + - + +
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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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313A LEU 3.0 12.8 + - - +
314A SER* 3.5 12.6 - - - +
316A ALA* 1.3 76.9 - - - +
318A THR* 1.3 63.3 + - + +
320A ASN* 3.2 18.7 + - - +
323A ASN* 3.3 54.8 - - - +
324A CYS* 3.5 16.8 + - - +
325A TYR* 3.7 18.9 - - + +
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Residues in contact with THR 318 (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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314A SER* 3.2 16.6 + - - +
315A TYR* 2.7 27.0 + - + -
317A LYS* 1.3 78.9 - - + +
319A ASN* 1.3 67.4 + - - +
320A ASN 3.4 3.7 + - - +
323A ASN* 5.3 2.7 - - - -
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Residues in contact with ASN 319 (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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315A TYR* 3.2 36.9 + - + +
316A ALA* 3.1 12.6 + - - +
317A LYS 3.1 0.6 - - - -
318A THR* 1.3 90.8 + - - +
320A ASN* 1.3 56.7 + - - +
321A SER 4.3 0.3 + - - -
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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