Contacts of the helix formed by residues 314 - 325 (chain A) in PDB entry 1P9W
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 THR 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A VAL* 4.9 0.9 - - - +
307A VAL* 4.4 7.4 - - - -
309A PRO* 6.0 2.5 - - + -
312A ASP* 3.2 33.2 + - - +
313A MSE 1.3 77.9 - - - +
315A PHE* 1.3 65.7 + - - +
316A ALA* 3.4 10.7 + - - +
317A ARG* 3.2 19.0 + - - +
318A GLY* 2.9 21.0 + - - -
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Residues in contact with PHE 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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291A VAL* 3.4 36.8 - - + +
293A ASP* 3.7 33.0 - - + -
307A VAL* 4.0 14.3 - - + +
314A THR* 1.3 73.1 - - - +
316A ALA* 1.3 57.7 + - - +
319A LEU* 3.0 33.4 + - - +
332A VAL* 3.6 18.2 - - + -
333A GLY* 3.4 16.8 - - - -
334A GLU* 3.9 25.4 - - + -
336A ARG* 3.8 32.3 - - + -
337A ASP* 5.8 1.1 - - - +
340A THR* 4.0 18.2 - - + +
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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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314A THR* 3.1 9.2 + - - +
315A PHE* 1.3 78.9 - - - +
317A ARG* 1.3 62.8 + - - +
319A LEU* 4.8 0.9 - - - -
320A ARG* 3.1 27.9 + - - +
337A ASP* 5.2 1.6 - - - +
339A GLU* 3.7 38.6 - - + +
340A THR* 3.8 12.2 + - - +
343A ILE* 3.7 18.5 - - + +
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Residues in contact with ARG 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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311A VAL* 2.9 27.9 + - - +
312A ASP* 3.0 29.9 + - - +
313A MSE 3.5 27.9 - - + +
314A THR* 3.2 17.9 + - - +
316A ALA* 1.3 78.7 - - - +
318A GLY* 1.3 63.6 - - - +
320A ARG* 3.3 19.9 + - + +
321A ALA* 3.0 22.2 + - - +
324A ARG* 5.5 0.3 + - - -
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Residues in contact with GLY 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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291A VAL* 4.5 13.5 - - - -
305A THR* 5.6 4.2 - - - +
313A MSE 4.1 18.1 - - - -
314A THR 2.9 14.4 + - - -
315A PHE 4.1 0.7 - - - -
317A ARG* 1.3 76.6 - - - +
319A LEU* 1.3 50.9 + - - +
321A ALA* 3.2 7.5 + - - +
322A ILE* 2.8 40.6 + - - +
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Residues in contact with LEU 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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291A VAL* 4.5 9.2 - - + +
315A PHE 3.0 18.0 + - - +
316A ALA 4.1 2.7 - - - +
318A GLY* 1.3 73.5 - - - +
320A ARG* 1.3 64.5 + - - +
322A ILE* 3.5 9.6 + - + +
323A LEU* 3.2 35.3 + - + +
330A VAL* 3.6 31.9 - - + -
332A VAL* 3.8 23.1 - - + -
340A THR* 4.0 21.3 - - + +
343A ILE* 3.6 24.2 - - + -
344A ALA* 4.0 16.4 - - - +
347A ALA* 5.2 4.3 - - + -
354A VAL* 5.7 0.4 - - + -
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Residues in contact with ARG 320 (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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316A ALA* 3.1 26.8 + - - +
317A ARG* 3.4 22.1 - - + +
319A LEU* 1.3 75.7 - - - +
321A ALA* 1.3 62.5 + - - +
323A LEU* 3.3 23.5 + - + +
324A ARG* 3.6 24.5 + - - +
339A GLU* 2.6 35.2 + - - +
343A ILE* 3.6 33.4 - - + +
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Residues in contact with ALA 321 (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 MSE 5.8 4.5 - - + -
317A ARG 3.0 12.9 + - - +
318A GLY* 3.4 11.4 - - - +
320A ARG* 1.3 71.9 - - - +
322A ILE* 1.3 68.0 + - + +
323A LEU 3.0 2.0 - - - -
324A ARG* 2.7 40.9 + - - +
325A GLN* 3.4 12.5 + - + +
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Residues in contact with ILE 322 (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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289A LEU* 3.6 42.6 - - + -
290A THR 4.1 21.5 - - - +
291A VAL* 4.9 3.8 - - + -
303A GLY 5.5 0.2 - - - +
305A THR* 4.5 12.3 - - + +
318A GLY 2.8 26.0 + - - +
319A LEU* 3.5 15.9 - - + +
321A ALA* 1.3 71.4 - - + +
323A LEU* 1.3 57.8 + - + +
325A GLN* 2.9 28.1 + - + +
327A PRO* 3.5 19.6 - - + +
330A VAL* 3.9 22.0 - - + -
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Residues in contact with LEU 323 (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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319A LEU* 3.2 20.0 - - + +
320A ARG* 3.3 10.7 + - + +
321A ALA 3.0 1.2 + - - -
322A ILE* 1.3 78.8 - - + +
324A ARG* 1.3 60.7 + - + +
325A GLN 3.2 0.7 + - - -
326A ASP* 3.6 9.2 + - - -
327A PRO* 3.9 7.6 - - + +
330A VAL* 4.4 16.6 - - + -
343A ILE* 3.8 24.7 - - + +
346A GLN* 6.2 1.1 - - + -
347A ALA* 3.6 33.4 - - + +
352A HIS* 3.9 25.0 + - + +
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Residues in contact with ARG 324 (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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317A ARG 5.5 0.6 + - - -
320A ARG* 3.6 28.4 + - - +
321A ALA* 2.7 37.8 + - - +
323A LEU* 1.3 73.4 - - + +
325A GLN* 1.3 66.3 + - - +
326A ASP* 3.4 2.6 + - - +
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Residues in contact with GLN 325 (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 ASN* 3.2 12.1 - - - +
289A LEU* 3.4 20.9 - - + +
321A ALA 3.8 12.5 + - - +
322A ILE* 2.9 13.7 + - + +
324A ARG* 1.3 86.3 + - - +
326A ASP* 1.3 69.1 + - - +
327A PRO* 3.5 2.2 - - - -
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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