Contacts of the helix formed by residues 304 - 319 (chain A) in PDB entry 2PFV
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 PHE 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR* 4.5 22.5 - + + -
236A SER 4.7 1.1 - - - -
237A SER* 3.2 31.9 - - - -
239A MET* 4.6 5.4 - - + -
240A ASN* 6.0 0.4 - - - -
290A ASN* 3.3 28.5 - - + -
294A VAL* 3.5 22.4 - - + -
301A PHE* 2.8 23.7 + + + +
303A PHE* 1.3 75.5 - - - +
305A SER* 1.3 57.2 + - - +
306A PHE 3.0 2.2 - - - -
307A GLU* 2.8 57.3 + - + +
308A LEU* 3.2 30.2 + - + -
385A TYR* 5.6 0.4 - - - -
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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
----------------------------------------------------------
291A LEU* 5.4 0.9 - - - -
294A VAL* 4.8 5.2 - - - +
301A PHE 4.2 0.8 + - - -
302A GLY 3.2 15.3 + - - -
304A PHE* 1.3 80.1 - - - +
306A PHE* 1.3 56.9 + - - +
308A LEU* 3.2 15.0 + - - +
309A VAL* 3.0 34.0 + - - +
337A VAL* 3.8 4.6 - - - +
340A VAL* 3.7 22.9 - - - -
341A THR* 3.2 25.4 - - - +
344A LEU* 3.3 13.7 - - - +
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Residues in contact with PHE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 3.5 32.3 + + + +
304A PHE 2.9 0.2 + - - -
305A SER* 1.3 83.5 + - - +
307A GLU* 1.3 60.3 + - - +
309A VAL* 3.6 7.6 + - + +
310A GLU* 3.5 23.2 + - - +
341A THR* 4.3 20.4 - - + -
344A LEU* 4.2 12.3 - - + -
345A PHE* 4.0 23.3 - + - -
382A PHE* 4.7 2.5 - + - -
385A TYR* 3.3 50.0 - + + -
388A GLY* 3.8 31.8 - - - -
389A CYS* 3.8 22.4 - - - -
392A ALA* 4.3 1.8 - - + -
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 5.9 0.3 - - - -
233A GLU 4.6 0.8 - - - +
234A LYS* 3.7 6.2 + - - +
235A GLY* 2.8 39.3 + - - -
236A SER 4.8 0.5 + - - +
237A SER* 4.5 1.6 - - - -
240A ASN* 4.0 22.6 + - - +
303A PHE 4.7 0.7 - - - +
304A PHE* 2.8 38.5 + - + +
306A PHE* 1.3 75.0 - - - +
308A LEU* 1.3 66.1 + - - +
309A VAL 3.2 0.4 - - - -
310A GLU* 3.1 18.8 - - + +
311A SER* 3.0 22.6 + - - -
385A TYR* 3.6 28.4 + - + -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 4.1 31.6 - - + -
287A PHE* 3.2 29.6 - - + +
290A ASN* 4.2 2.2 - - + -
291A LEU* 3.9 42.8 - - + +
294A VAL* 4.6 2.0 - - + -
304A PHE* 3.2 44.4 + - + +
305A SER* 3.6 13.2 - - - +
307A GLU* 1.3 76.9 - - - +
309A VAL* 1.3 57.2 + - - +
311A SER* 3.2 4.5 - - - -
312A ILE* 3.0 25.3 + - - +
337A VAL* 3.9 5.2 - - + -
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER 3.0 21.6 + - - +
306A PHE* 3.6 10.3 - - + +
307A GLU 3.2 0.2 - - - -
308A LEU* 1.3 74.2 - - - +
310A GLU* 1.3 67.7 + - - +
312A ILE* 3.2 8.4 - - + +
313A ASN* 2.9 45.6 + - - +
337A VAL* 3.6 18.6 - - + +
338A ARG* 5.6 1.1 - - - -
341A THR* 3.6 23.8 - - + +
388A GLY* 6.5 1.3 - - - -
391A GLY 6.6 0.2 - - - -
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ASN* 4.6 13.9 + - - +
306A PHE 3.5 8.7 + - - +
307A GLU* 3.1 32.0 - - - +
309A VAL* 1.3 81.4 - - - +
311A SER* 1.3 56.4 + - - +
313A ASN* 3.6 7.7 - - - +
314A ASP* 2.8 45.9 + - - +
387A ASN* 6.2 0.2 - - - +
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET* 4.1 11.4 - - - +
240A ASN* 5.6 4.0 - - - -
243A THR* 2.7 31.7 + - - +
283A TYR* 2.6 22.6 + - - -
287A PHE* 4.9 0.7 - - - -
307A GLU 3.0 15.5 + - - -
308A LEU* 3.2 15.0 - - - -
310A GLU* 1.3 78.3 - - - +
312A ILE* 1.3 62.8 + - - +
314A ASP* 3.1 8.0 + - - +
315A VAL* 3.0 23.2 + - - +
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Residues in contact with ILE 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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283A TYR* 3.3 17.6 + - + -
287A PHE* 3.9 15.9 - - + -
308A LEU 3.0 13.0 + - - +
309A VAL* 3.2 16.6 - - + +
311A SER* 1.3 80.1 - - - +
313A ASN* 1.3 73.7 + - - +
315A VAL* 4.4 3.1 - - + -
316A LYS* 3.0 35.2 + - + +
330A LEU* 3.4 44.0 - - + +
333A CYS* 4.5 5.8 - - + -
334A THR* 3.5 26.9 - - + +
337A VAL* 4.3 9.0 - - + -
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 2.9 39.1 + - - +
310A GLU* 3.6 8.7 - - - +
312A ILE* 1.3 86.3 - - - +
314A ASP* 1.3 60.5 + - - +
316A LYS* 3.4 4.6 + - - +
317A LYS* 2.9 31.3 + - - +
320A ARG* 5.1 2.1 + - - -
334A THR* 5.1 9.9 + - - +
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Residues in contact with ASP 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 4.4 6.0 - - + +
247A LEU* 3.6 25.9 - - + +
310A GLU* 2.8 35.2 + - - +
311A SER* 3.1 7.4 + - - +
313A ASN* 1.3 79.2 - - - +
315A VAL* 1.3 61.7 + - - +
317A LYS* 3.4 12.8 + - - +
318A SER* 3.1 23.4 + - - -
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 4.1 9.6 - - + -
246A LEU* 4.2 11.0 - - + -
247A LEU* 3.7 17.9 - - + -
250A ILE* 4.7 4.0 - - + -
280A ILE* 4.0 17.3 - - + -
283A TYR* 3.9 23.8 - - + -
311A SER 3.0 16.8 + - - +
312A ILE* 3.8 8.7 - - + +
313A ASN 3.3 0.2 - - - -
314A ASP* 1.3 76.4 - - - +
316A LYS* 1.3 62.6 + - - +
318A SER* 2.6 22.3 + - - +
319A LEU* 3.1 24.6 + - + +
330A LEU* 4.1 13.2 - - + -
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Residues in contact with LYS 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 ILE* 3.0 37.8 + - + +
313A ASN* 3.8 6.1 - - - +
315A VAL* 1.3 75.5 - - - +
317A LYS* 1.3 61.8 + - - +
319A LEU* 3.1 18.5 + - - +
320A ARG* 3.3 22.7 + - - +
327A TYR* 4.3 18.7 + - + +
330A LEU* 4.2 16.2 - - + -
334A THR* 4.7 6.1 - - - +
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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 ASN 2.9 18.7 + - - +
314A ASP* 3.6 12.6 - - - +
316A LYS* 1.3 77.3 - - - +
318A SER* 1.3 60.7 + - - +
320A ARG* 3.1 47.6 + - - +
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Residues in contact with SER 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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247A LEU* 3.7 17.3 - - - +
250A ILE* 3.4 33.0 - - - +
251A ALA* 6.5 0.4 - - - -
314A ASP 3.1 12.2 + - - -
315A VAL 2.6 19.5 + - - -
317A LYS* 1.3 77.1 - - - +
319A LEU* 1.3 57.3 + - - +
320A ARG 3.4 0.4 - - - +
322A LYS* 2.9 27.2 + - - -
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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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250A ILE* 4.2 25.4 - - + -
276A LEU* 4.2 11.4 - - + -
280A ILE* 3.8 17.9 - - + -
315A VAL* 3.4 14.4 - - + +
316A LYS* 3.1 10.1 + - - +
318A SER* 1.3 80.1 - - - +
320A ARG* 1.3 65.7 + - - +
321A GLY 3.2 0.5 + - - -
322A LYS* 2.9 38.3 + - + +
324A LEU* 3.9 22.7 - - + -
327A TYR* 4.5 13.1 - - + -
330A LEU* 3.4 33.7 - - + -
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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