Contacts of the helix formed by residues 304 - 321 (chain A) in PDB entry 4FWF
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 PRO 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASP 5.8 0.7 - - - +
289A MET* 3.8 22.9 - - + +
300A TYR* 3.3 21.1 - - + +
301A SER 4.7 2.5 - - - +
302A ARG 3.7 7.2 - - - +
303A ASP* 1.3 87.6 - - - +
305A THR* 1.3 60.1 + - + +
306A MET 3.2 2.5 - - - -
307A TYR* 2.7 28.9 + - - +
308A LEU* 3.0 24.6 + - + -
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PRO* 3.1 29.1 - - + +
209A PRO 5.1 4.2 - - - +
210A LEU* 5.6 1.6 - - + -
226A ASP 4.3 18.4 - - - +
227A CYS 5.2 6.3 - - - +
228A VAL 5.6 0.2 - - - -
229A GLY* 4.2 13.9 - - - +
303A ASP* 3.0 18.8 + - - +
304A PRO* 1.3 81.3 - - + +
306A MET* 1.3 61.3 + - - +
308A LEU* 3.9 11.1 - - + +
309A ALA* 3.0 25.5 + - - +
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Residues in contact with MET 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TYR* 3.7 40.9 + - + +
209A PRO* 3.9 19.2 - - + +
300A TYR* 4.0 14.4 - - + +
304A PRO 3.0 1.0 + - - -
305A THR* 1.3 78.6 + - - +
307A TYR* 1.3 63.8 + - - +
309A ALA* 3.6 5.1 + - - +
310A LEU* 3.3 29.8 + - + +
341A VAL* 4.5 1.3 - - - -
344A ARG* 3.5 29.2 - - + +
345A CYS* 3.6 21.5 - - - +
348A GLU* 3.4 40.6 - - + -
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Residues in contact with TYR 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 3.8 23.1 - - + -
293A GLU* 2.7 50.2 + - + +
297A PHE* 3.6 24.2 - + - -
300A TYR* 4.0 37.8 - + + -
304A PRO 2.7 16.4 + - - +
306A MET* 1.3 72.9 - - - +
308A LEU* 1.3 64.4 + - + +
310A LEU* 3.0 4.9 + - - +
311A ARG* 2.9 44.9 + - + +
352A ILE* 3.7 35.2 - - + +
355A PHE* 3.9 13.9 - - - -
356A MET* 4.9 1.7 - - - +
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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
----------------------------------------------------------
227A CYS 5.2 4.7 - - - +
228A VAL* 4.6 7.0 - - - +
286A PRO 3.7 10.3 - - - +
287A ASP* 3.4 30.3 - - - +
288A VAL* 3.7 15.3 - - - -
289A MET* 3.7 14.6 - - + +
304A PRO* 3.0 32.9 + - + +
305A THR* 4.2 10.3 - - + +
307A TYR* 1.3 78.8 - - + +
309A ALA* 1.3 59.9 + - - +
311A ARG* 3.5 38.6 - - - +
312A ASN* 2.9 34.3 + - - +
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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
----------------------------------------------------------
209A PRO* 5.3 2.9 - - + +
211A LEU* 4.2 19.7 - - + +
214A SER* 5.0 2.6 + - - -
228A VAL 4.2 8.7 + - - -
229A GLY* 3.8 25.6 - - - +
305A THR 3.0 19.4 + - - +
306A MET* 3.8 6.5 - - - +
308A LEU* 1.3 77.3 - - - +
310A LEU* 1.3 60.1 + - + +
312A ASN* 4.0 2.5 - - - +
313A LEU* 3.1 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
----------------------------------------------------------
211A LEU* 4.4 14.6 - - + -
306A MET* 3.3 35.4 + - + +
307A TYR 3.0 3.2 + - - +
309A ALA* 1.3 77.4 - - + +
311A ARG* 1.3 65.8 + - - +
313A LEU* 3.4 5.5 + - + +
314A ILE* 3.0 31.7 + - - +
335A ILE* 4.0 26.0 - - + -
345A CYS* 3.7 27.1 - - + +
348A GLU* 4.5 0.2 - - + -
349A VAL* 3.8 26.7 - - + +
352A ILE* 3.9 24.0 - - + -
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 3.4 22.2 - - - +
285A ARG 2.4 28.6 + - - -
286A PRO* 3.3 8.1 - - - +
288A VAL 3.4 13.3 + - - -
290A GLU* 4.2 1.6 - - - +
293A GLU* 2.8 43.0 + - - +
307A TYR* 2.9 28.7 + - + +
308A LEU* 3.5 21.9 - - - +
310A LEU* 1.3 76.5 - - - +
312A ASN* 1.3 79.7 + - - +
314A ILE* 3.2 3.6 + - - +
315A LEU* 2.9 34.3 + - + +
352A ILE* 4.6 4.5 - - + +
356A MET* 3.8 30.7 - - + +
361A LEU* 6.4 0.2 - - - -
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Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA* 3.5 20.8 - - + +
220A LEU* 4.3 3.9 - - + +
228A VAL* 3.5 14.8 + - - +
272A PHE* 3.3 30.7 - - + -
286A PRO* 3.0 36.7 + - - +
308A LEU 2.9 21.7 + - - +
309A ALA* 4.0 3.6 - - - +
311A ARG* 1.3 101.3 + - - +
313A LEU* 1.3 62.3 + - - +
315A LEU* 3.7 0.4 + - - -
316A ALA* 3.2 15.9 + - - +
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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
----------------------------------------------------------
211A LEU* 4.5 9.2 - - + -
214A SER* 3.3 22.9 + - - +
215A VAL* 3.7 22.7 - - + +
216A ALA* 4.3 6.5 - - - +
309A ALA 3.1 18.3 + - - +
310A LEU* 3.6 10.5 - - + +
311A ARG 3.2 0.2 - - - -
312A ASN* 1.3 75.7 - - - +
314A ILE* 1.3 59.9 + - + +
316A ALA* 3.0 5.7 + - - +
317A LEU* 2.8 38.1 + - + +
331A CYS* 4.6 7.9 - - + +
334A HIS* 4.1 28.0 - - + +
335A ILE* 4.1 26.0 - - + -
349A VAL* 5.5 1.3 - - + -
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Residues in contact with ILE 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 3.0 18.5 + - - +
311A ARG 3.6 3.1 - - - +
313A LEU* 1.3 77.9 - - + +
315A LEU* 1.3 66.2 + - - +
317A LEU* 3.1 4.0 + - - -
318A TRP* 2.8 22.5 + - - +
326A LEU* 3.5 21.5 - - + +
331A CYS* 4.1 19.7 - - + -
349A VAL* 4.0 30.1 - - + +
352A ILE* 4.2 22.2 - - + -
353A LEU* 4.3 15.5 - - + +
356A MET* 3.7 15.0 - - + -
362A ILE* 3.6 17.9 - - + -
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO* 4.7 11.2 - - + +
272A PHE* 4.0 27.8 - - + -
284A VAL* 4.8 13.0 - - + -
311A ARG* 2.9 28.2 + - + +
312A ASN 3.9 4.5 - - - +
314A ILE* 1.3 76.2 - - - +
316A ALA* 1.3 57.0 + - - +
318A TRP* 3.3 1.0 + - - +
319A TYR* 2.9 56.0 + - + -
356A MET* 3.5 21.1 - - + -
361A LEU* 4.2 10.5 - - + +
362A ILE* 3.5 23.1 - - + -
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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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215A VAL* 3.7 22.0 - - + +
216A ALA* 3.8 19.3 - - + +
219A LEU* 4.0 12.3 - - + -
265A MET* 4.0 10.5 - - + +
271A PRO* 6.1 0.2 - - - -
272A PHE* 5.1 1.3 - - + -
312A ASN 3.2 11.0 + - - +
313A LEU 3.0 8.8 + - - +
315A LEU* 1.3 76.5 - - - +
317A LEU* 1.3 65.5 + - - +
319A TYR 3.2 0.7 + - - -
320A THR* 3.0 30.8 + - + +
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Residues in contact with LEU 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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215A VAL* 3.9 27.4 - - + -
313A LEU* 2.8 31.3 + - + +
314A ILE 3.6 7.0 - - - +
316A ALA* 1.3 73.7 - - - +
318A TRP* 1.3 62.2 + - - +
320A THR* 3.3 15.2 + - - +
321A ASN* 3.3 17.2 + - - +
326A LEU* 3.7 20.0 - - + +
330A LYS 4.1 4.7 - - - +
331A CYS* 3.7 40.6 - - + +
334A HIS* 4.1 19.7 - - + +
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Residues in contact with TRP 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 ILE 2.8 6.5 + - - +
315A LEU 3.4 6.1 - - - +
317A LEU* 1.3 78.2 - - - +
319A TYR* 1.3 100.3 + + - +
321A ASN 3.2 28.2 - - - -
322A CYS* 3.3 35.1 + - + +
324A GLU 4.0 10.3 - - - -
326A LEU* 4.1 8.7 - - + +
361A LEU 3.7 15.9 + - - -
362A ILE* 3.4 23.1 - - + -
363A ASN* 3.4 35.7 - - - -
364A THR* 3.4 43.2 + - - -
367A LEU* 4.3 5.6 - - + -
449A LEU* 3.9 21.7 - - + +
453A GLN* 3.8 0.2 - - - -
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Residues in contact with TYR 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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264A GLY 4.4 2.3 - - - +
265A MET* 3.4 37.0 - - + +
269A PHE* 3.6 57.4 - + + -
271A PRO* 4.0 28.2 - - + +
315A LEU* 2.9 43.3 + - + +
316A ALA 3.2 0.4 + - - -
318A TRP* 1.3 103.2 + + - +
320A THR* 1.3 58.8 + - - +
321A ASN 3.4 0.2 - - - -
322A CYS* 4.8 3.3 - - - +
361A LEU* 4.1 8.8 + - - -
444A ASN* 5.6 8.0 + - - -
449A LEU* 4.5 10.5 - - + -
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A VAL* 4.5 15.5 - - + +
219A LEU* 5.9 0.2 - - + -
262A VAL* 5.4 2.7 - - + -
263A PRO 5.3 4.7 - - - +
264A GLY* 4.1 17.6 - - - +
265A MET* 3.6 24.9 - - + -
316A ALA* 3.0 21.4 + - + +
317A LEU* 3.3 14.4 + - - +
318A TRP 3.2 0.2 - - - -
319A TYR* 1.3 77.4 - - - +
321A ASN* 1.3 60.8 + - - +
322A CYS 4.1 0.2 - - - -
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU 3.3 12.1 + - - +
318A TRP* 3.2 10.2 + - - +
320A THR* 1.3 83.7 - - - +
322A CYS* 1.3 57.8 + - - +
323A LYS* 3.4 10.3 + - - +
324A GLU* 2.8 57.6 + - - +
326A LEU* 6.1 0.5 - - - +
330A LYS* 5.7 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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