Contacts of the helix formed by residues 308 - 327 (chain A) in PDB entry 4F4W
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 SER 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A TYR* 3.5 1.1 + - - -
281A ILE* 6.2 2.0 - - - -
306A GLY 3.8 3.8 + - - -
307A ILE* 1.3 78.9 - - - +
309A LYS* 1.3 66.7 + - - +
310A GLU* 3.7 14.9 + - - +
311A THR* 3.1 30.6 + - - -
312A ALA 3.0 18.2 + - - -
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Residues in contact with LYS 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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270A ILE* 4.3 5.4 - - + -
271A GLU* 2.7 36.2 + - - +
274A TYR* 3.7 47.2 - - + -
308A SER* 1.3 73.8 - - - +
310A GLU* 1.3 77.1 + - - +
312A ALA* 3.3 4.0 + - - +
313A TYR* 3.1 48.5 + - + +
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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
----------------------------------------------------------
308A SER* 3.7 12.1 - - - +
309A LYS* 1.3 100.2 + - - +
311A THR* 1.3 61.1 + - - +
313A TYR* 3.3 25.3 + - + +
314A SER* 3.4 12.8 + - - -
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Residues in contact with THR 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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303A PHE* 4.7 21.8 - - + -
305A HIS* 5.2 9.5 + - - +
307A ILE* 4.1 14.8 - - + -
308A SER* 3.1 25.4 + - - -
310A GLU* 1.3 73.9 - - - +
312A ALA* 1.3 61.0 + - - +
314A SER* 3.2 8.2 + - - +
315A GLU* 2.9 30.0 + - + +
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Residues in contact with ALA 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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270A ILE* 4.0 7.0 - - + -
274A TYR* 3.6 35.2 - - + +
285A ILE* 3.7 7.5 - - - +
307A ILE* 3.5 10.2 - - + +
308A SER 3.0 4.4 + - - -
309A LYS 3.3 10.5 - - - +
310A GLU 3.2 0.2 - - - -
311A THR* 1.3 77.1 - - - +
313A TYR* 1.3 63.0 + - - +
315A GLU* 4.9 0.7 - - - -
316A SER* 2.8 28.2 + - - -
338A PHE* 3.9 14.6 - - + -
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Residues in contact with TYR 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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267A PHE* 3.5 52.6 + + + -
270A ILE* 3.6 21.1 - - + -
271A GLU* 2.0 35.3 + - - +
309A LYS* 3.1 42.9 + - + +
310A GLU* 3.6 18.2 - - + +
311A THR 3.2 0.2 - - - -
312A ALA* 1.3 76.4 - - - +
314A SER* 1.3 62.7 + - - +
316A SER* 2.8 20.9 + - - -
317A VAL* 3.3 14.3 + - - +
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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 GLU 3.4 9.6 + - - -
311A THR* 3.2 15.1 + - - +
313A TYR* 1.3 78.9 - - - +
315A GLU* 1.3 65.2 + - - +
317A VAL* 3.2 16.3 + - - +
318A LYS* 3.4 23.0 + - - +
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Residues in contact with GLU 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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285A ILE* 4.0 15.9 - - + -
301A ARG* 3.1 36.0 + - - -
303A PHE* 3.5 34.3 - - + -
307A ILE* 6.1 0.2 - - + -
311A THR* 2.9 19.7 + - + +
312A ALA* 4.3 1.3 - - - +
314A SER* 1.3 75.2 + - - +
316A SER* 1.3 66.1 + - - +
318A LYS* 3.1 27.4 + - - +
319A LEU* 3.0 38.4 + - + +
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Residues in contact with SER 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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266A LEU* 3.6 15.8 - - - +
267A PHE* 4.0 2.4 - - - -
270A ILE* 3.3 23.4 - - - +
285A ILE* 3.9 8.7 - - - +
287A VAL* 3.6 26.6 - - - +
312A ALA 2.8 16.6 + - - -
313A TYR* 2.8 19.2 + - - -
315A GLU* 1.3 77.2 - - - +
317A VAL* 1.3 56.7 + - - +
319A LEU* 3.2 1.0 + - - -
320A LEU* 2.9 30.0 + - - +
336A VAL* 4.5 0.7 - - - -
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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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259A LEU* 4.1 26.7 - - + -
263A LYS* 4.0 17.0 - - + +
266A LEU* 4.7 3.6 - - + -
267A PHE* 3.8 26.5 - - + -
313A TYR 3.4 15.0 - - - +
314A SER* 3.2 8.9 + - - +
315A GLU 3.1 0.6 - - - -
316A SER* 1.3 78.3 + - - +
318A LYS* 1.3 56.7 + - + +
320A LEU* 3.3 6.5 + - + +
321A GLN* 2.9 41.2 + - - +
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Residues in contact with LYS 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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301A ARG* 4.8 6.9 - - - +
314A SER* 3.4 18.5 + - - +
315A GLU* 3.1 35.0 + - - +
317A VAL* 1.3 79.4 - - + +
319A LEU* 1.3 61.8 + - - +
321A GLN* 3.4 17.0 + - - +
322A LYS* 3.1 22.3 + - - +
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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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285A ILE* 3.7 33.2 - - + +
287A VAL* 3.7 24.7 - - + -
299A ARG* 3.6 31.8 - - + +
300A GLY* 3.8 21.1 - - - +
301A ARG* 4.4 2.2 - - + +
315A GLU* 3.0 36.2 + - + +
316A SER 3.7 0.7 - - - +
317A VAL 3.2 0.2 - - - -
318A LYS* 1.3 74.4 - - - +
320A LEU* 1.3 63.4 + - - +
322A LYS* 3.1 24.7 + - - +
323A ILE* 3.0 26.9 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.6 27.8 - - + +
262A ILE* 3.6 29.6 - - + -
263A LYS* 5.1 4.3 - - + +
266A LEU* 4.1 18.4 - - + -
287A VAL* 4.4 7.9 - - + +
316A SER 2.9 16.3 + - - +
317A VAL* 3.6 6.1 - - - +
319A LEU* 1.3 73.3 - - - +
321A GLN* 1.3 66.5 + - - +
323A ILE* 3.1 8.2 + - + +
324A LEU* 2.9 26.5 + - + +
331A ILE* 3.9 28.0 - - + -
334A ILE* 4.1 14.8 - - + -
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Residues in contact with GLN 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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259A LEU* 4.1 26.5 - - + +
317A VAL* 2.9 36.0 + - - +
318A LYS* 3.6 18.8 + - - +
320A LEU* 1.3 77.2 - - - +
322A LYS* 1.3 57.3 + - - +
324A LEU* 3.2 10.5 + - + +
325A GLU* 2.8 32.0 + - - +
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Residues in contact with LYS 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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299A ARG* 3.8 25.6 - - + +
300A GLY 5.2 3.6 + - - -
318A LYS 3.1 15.0 + - - +
319A LEU* 3.1 26.1 + - - +
321A GLN* 1.3 75.9 - - - +
323A ILE* 1.3 63.4 + - - +
325A GLU* 3.1 13.9 + - + +
326A GLU* 2.9 46.3 + - - +
8P A 4.8 4.8 + - - +
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Residues in contact with ILE 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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287A VAL* 3.7 42.0 - - + +
289A ALA* 4.0 21.1 - - + -
291A THR* 6.1 1.6 - - + -
297A VAL* 3.9 33.2 - - + +
299A ARG* 3.5 26.7 - - + +
319A LEU 3.0 12.3 + - - +
320A LEU* 3.5 10.5 - - + +
322A LYS* 1.3 75.6 - - - +
324A LEU* 1.3 59.6 + - - +
326A GLU* 3.2 1.2 + - - -
327A ASP* 2.8 36.6 + - + +
331A ILE* 4.4 12.8 - - + -
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Residues in contact with LEU 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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257A ARG* 2.9 75.3 + - + +
259A LEU* 4.0 26.7 - - + +
262A ILE* 4.6 4.0 - - + -
320A LEU* 2.9 25.0 + - + +
321A GLN* 3.6 9.6 - - + +
323A ILE* 1.3 76.9 - - - +
325A GLU* 1.3 62.0 + - - +
327A ASP 3.1 10.6 - - - +
328A GLU* 4.9 0.5 - - - +
331A ILE* 3.7 25.8 - - + -
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Residues in contact with GLU 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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321A GLN 2.8 16.8 + - - +
322A LYS* 3.1 11.3 + - - +
324A LEU* 1.3 79.7 - - - +
326A GLU* 1.3 75.4 + - + +
327A ASP 3.7 0.9 + - - -
328A GLU* 5.7 3.1 - - - +
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Residues in contact with GLU 326 (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 ARG* 2.8 39.8 + - - +
322A LYS* 2.9 33.6 + - - +
323A ILE 4.4 0.4 - - - +
325A GLU* 1.3 94.7 - - + +
327A ASP* 1.3 60.6 + - - +
328A GLU* 5.9 1.1 - - - -
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ARG* 2.5 25.5 + - - -
291A THR* 4.3 3.6 - - - +
297A VAL* 3.7 18.3 - - + +
299A ARG* 5.9 0.9 - - - +
323A ILE* 2.8 24.5 + - + +
324A LEU* 3.1 9.1 - - - +
325A GLU 3.5 0.6 - - - -
326A GLU* 1.3 81.8 - - - +
328A GLU* 1.3 53.9 + - - +
329A ARG* 2.7 72.4 + - - +
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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
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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