Contacts of the helix formed by residues 302 - 317 (chain A) in PDB entry 1U1H
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A ALA 3.8 1.2 + - - -
301A ASN* 1.3 77.1 + - - +
303A PHE* 1.3 63.2 + - - +
304A ALA* 3.4 9.8 + - - +
305A ALA* 3.3 31.6 + - + +
306A SER* 2.9 20.5 + - - +
384A LEU* 3.2 29.8 - - + +
388A ARG* 3.0 21.4 + - - +
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ASN* 3.2 16.8 + - + -
302A ASP* 1.3 70.2 - - - +
304A ALA* 1.3 66.5 + - - +
306A SER* 3.2 1.9 + - - -
307A LEU* 2.9 25.1 + - - +
359A VAL* 6.4 1.1 - - + -
360A GLU* 3.5 44.4 - - + -
363A ALA* 4.1 19.1 - - + -
364A LEU* 4.0 10.3 - - + +
376A LEU* 4.3 16.2 - - + -
377A PHE* 3.7 43.7 - + + +
380A ASN* 3.2 45.4 + - + +
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Residues in contact with ALA 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 ASP* 3.3 9.9 + - - +
303A PHE* 1.3 80.4 - - - +
305A ALA* 1.3 63.5 + - - +
307A LEU* 3.1 6.8 + - - +
308A SER* 3.0 21.2 + - - -
377A PHE* 5.0 3.7 - - - -
380A ASN* 4.8 0.4 + - - -
384A LEU* 5.4 1.5 - - + +
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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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302A ASP* 3.2 30.8 + - + +
304A ALA* 1.3 77.6 - - - +
306A SER* 1.3 64.8 + - - +
308A SER* 3.1 9.7 + - - -
309A THR* 3.0 25.7 + - - +
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Residues in contact with SER 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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292A VAL* 2.9 33.8 - - - +
301A ASN* 2.9 27.6 + - - -
302A ASP* 2.9 12.2 + - - +
303A PHE 3.6 4.0 - - - -
305A ALA* 1.3 75.7 - - - +
307A LEU* 1.3 59.0 + - - +
309A THR* 3.1 5.8 + - - -
310A LEU* 2.8 35.0 + - - +
364A LEU* 3.7 15.5 - - - -
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Residues in contact with LEU 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 PHE 2.9 10.4 + - - +
304A ALA* 3.5 9.9 - - - +
306A SER* 1.3 74.7 - - - +
308A SER* 1.3 63.7 + - - +
310A LEU* 3.2 6.1 + - + -
311A GLN* 2.9 48.3 + - + +
364A LEU* 4.3 7.6 - - + +
367A ALA* 3.9 20.4 - - + +
368A LEU* 3.5 36.8 - - + +
372A LYS* 4.4 13.9 - - + +
377A PHE* 3.5 33.4 - - + -
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Residues in contact with SER 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 ALA 3.0 12.3 + - - -
305A ALA* 3.3 12.3 - - - -
307A LEU* 1.3 76.7 - - - +
309A THR* 1.3 62.8 + - - +
311A GLN* 3.9 11.5 + - - +
312A ALA* 3.4 19.1 + - - +
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Residues in contact with THR 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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268A LEU* 4.8 8.5 - - + -
275A LEU* 4.5 20.4 - - + -
292A VAL* 4.8 9.4 - - + -
305A ALA 3.0 14.3 + - - -
306A SER* 3.4 9.8 - - - -
308A SER* 1.3 74.9 - - - +
310A LEU* 1.3 66.3 + - - +
312A ALA* 3.2 8.3 + - + +
313A LEU* 3.1 37.2 + - + +
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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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290A ALA* 3.6 31.0 - - + -
292A VAL* 3.8 13.5 - - + -
306A SER* 2.8 25.1 + - - +
307A LEU* 3.8 4.7 - - - +
309A THR* 1.3 72.8 - - - +
311A GLN* 1.3 58.4 + - - +
313A LEU* 3.3 7.7 + - + +
314A GLU* 2.9 26.5 + - - +
322A LEU* 4.1 18.7 - - + +
324A VAL* 3.8 26.2 - - + -
364A LEU* 4.0 22.4 - - + +
368A LEU* 3.7 30.7 - - + -
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Residues in contact with GLN 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 LEU* 2.9 48.5 + - - +
308A SER* 3.9 8.5 - - - +
310A LEU* 1.3 74.0 - - - +
312A ALA* 1.3 66.2 + - - +
314A GLU* 3.0 30.6 + - - +
315A GLY* 3.1 5.7 + - - -
367A ALA 5.6 2.6 + - - -
368A LEU* 3.8 17.7 - - + +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A LYS* 5.8 8.3 - - - +
308A SER 3.4 11.0 + - - +
309A THR* 3.2 11.3 + - - +
311A GLN* 1.3 78.0 - - - +
313A LEU* 1.3 60.6 + - + +
315A GLY* 3.0 17.9 + - - +
316A ILE* 3.4 14.9 + - - +
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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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268A LEU* 3.8 27.8 - - + -
275A LEU* 3.7 22.7 - - + -
278A VAL* 4.1 13.0 - - + -
279A LYS* 6.0 3.8 - - + -
288A LEU* 4.0 22.0 - - + -
290A ALA* 4.0 15.3 - - + -
309A THR* 3.1 24.1 + - + +
310A LEU* 3.5 9.0 - - - +
311A GLN 3.2 0.2 - - - -
312A ALA* 1.3 75.5 - - + +
314A GLU* 1.3 65.5 - - - +
316A ILE* 3.0 21.1 + - + +
317A VAL* 3.0 15.4 + - - +
318A GLY 3.8 0.5 + - - -
322A LEU* 3.7 16.6 - - + +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A LEU 2.9 11.8 + - - +
311A GLN* 3.0 27.1 + - - +
313A LEU* 1.3 77.2 - - - +
315A GLY* 1.3 59.5 + - - +
317A VAL 2.9 5.7 - - - +
318A GLY* 2.8 54.5 + - - +
322A LEU* 4.3 8.3 - - + +
368A LEU* 3.9 35.6 - - - +
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Residues in contact with GLY 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 GLN 3.1 7.7 + - - -
312A ALA* 3.0 10.6 + - - -
314A GLU* 1.3 78.8 - - - +
316A ILE* 1.3 61.4 + - - +
317A VAL 3.4 1.2 + - - +
319A LYS* 5.6 2.6 + - - -
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A VAL* 4.3 21.3 - - + +
279A LYS* 4.5 25.8 - - + +
282A PHE* 4.2 21.9 - - + +
312A ALA 3.7 13.7 - - - +
313A LEU* 3.0 15.8 + - + +
315A GLY* 1.3 79.3 - - - +
317A VAL* 1.3 67.7 + - + +
319A LYS* 5.3 2.4 + - - -
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Residues in contact with VAL 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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282A PHE* 4.1 20.4 - - + -
283A PRO 5.5 0.2 - - - +
284A GLU 4.8 12.3 - - - +
285A GLY* 5.4 0.7 - - - -
286A LYS 3.8 11.7 - - - +
288A LEU* 4.8 15.5 - - + -
313A LEU 3.0 9.5 + - - +
314A GLU 2.9 6.4 + - - +
315A GLY 4.6 0.9 - - - +
316A ILE* 1.3 92.8 - - + +
318A GLY* 1.3 53.2 + - - +
319A LYS* 2.4 46.1 + - + +
321A LYS* 3.3 34.5 - - + -
322A LEU* 5.8 1.6 - - + -
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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