Contacts of the helix formed by residues 309 - 330 (chain A) in PDB entry 4G1T
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 LYS 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A GLY* 1.3 70.2 - - - +
310A ARG* 1.3 60.0 + - - +
312A LEU* 4.6 14.1 - - + +
313A LEU* 2.3 59.3 + - + +
346A LEU 5.4 5.7 + - - -
348A ASP* 5.1 9.7 + - - -
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Residues in contact with ARG 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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308A GLY 3.4 1.0 - - - -
309A LYS* 1.3 77.8 - - - +
311A LYS* 1.3 81.9 + - + +
313A LEU* 3.4 8.2 - - - +
314A GLU* 2.6 49.2 + - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 5.6 12.1 - - + -
308A GLY* 3.3 12.9 + - - +
310A ARG* 1.3 101.4 - - + +
312A LEU* 1.3 58.8 + - + +
314A GLU* 4.3 5.6 - - - +
315A LEU* 2.6 50.5 + - + +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 4.0 27.8 - - + +
298A VAL* 4.4 17.7 - - + -
299A MET* 4.1 24.9 - - + -
308A GLY 2.9 41.0 + - - +
309A LYS* 4.2 17.0 - - + +
311A LYS* 1.3 72.8 - - + +
313A LEU* 1.3 53.4 - - + +
315A LEU* 4.4 5.2 - - + -
316A ILE* 2.6 55.4 + - + +
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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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309A LYS* 2.3 51.9 + - + +
310A ARG* 3.4 7.6 - - - +
312A LEU* 1.3 80.9 - - + +
314A GLU* 1.3 56.7 + - - +
316A ILE* 4.3 4.2 - - + +
317A GLY* 3.2 19.2 + - - -
347A ALA* 4.7 27.4 - - + +
348A ASP* 6.5 0.2 - - - -
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Residues in contact with GLU 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 ARG* 2.6 32.1 + - + +
311A LYS* 3.9 5.1 - - - +
313A LEU* 1.3 73.5 - - - +
315A LEU* 1.3 69.9 + - - +
317A GLY* 3.0 10.3 + - - -
318A HIS* 2.8 50.6 + - + -
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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
----------------------------------------------------------
291A TYR* 4.0 29.2 - - + +
294A LYS* 3.6 49.4 - - + +
295A VAL* 4.3 18.2 - - + +
298A VAL* 4.3 12.8 - - + -
311A LYS* 2.6 35.4 + - + +
312A LEU* 4.0 4.3 - - + +
314A GLU* 1.3 78.1 + - - +
316A ILE* 1.3 60.8 + - - +
317A GLY 2.9 1.1 - - - -
318A HIS* 2.8 23.9 + - + +
319A ALA* 3.2 12.1 + - - +
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Residues in contact with ILE 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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295A VAL* 4.1 24.0 - - + -
312A LEU* 2.6 45.5 + - + +
313A LEU* 4.3 4.7 - - + +
315A LEU* 1.3 73.1 - - - +
317A GLY* 1.3 61.5 + - - +
319A ALA* 3.8 4.8 + - - +
320A VAL* 3.2 31.4 + - + +
343A LEU* 3.7 24.7 - - + +
344A HIS* 5.4 0.7 - - + -
346A LEU* 3.7 35.2 - - + -
347A ALA* 4.0 22.9 - - + +
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Residues in contact with GLY 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 LEU 3.2 13.7 + - - -
314A GLU* 3.0 10.1 + - - -
315A LEU 2.9 1.2 - - - -
316A ILE* 1.3 79.5 - - - +
318A HIS* 1.3 57.6 + - - +
320A VAL* 3.3 6.1 + - - +
321A ALA* 3.0 28.2 + - - +
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Residues in contact with HIS 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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271A LYS* 6.0 0.4 - - - -
291A TYR* 3.6 44.6 - + + -
314A GLU* 2.8 54.4 + - + -
315A LEU* 2.8 10.6 + - + +
317A GLY* 1.3 73.4 - - - +
319A ALA* 1.3 66.4 + - - +
320A VAL 3.0 1.9 + - - -
321A ALA* 3.1 6.1 + - - +
322A HIS* 3.1 35.7 + + - -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A GLY* 3.4 25.8 - - - +
291A TYR* 3.6 19.4 - - + +
292A ARG* 4.0 6.7 - - - +
295A VAL* 5.5 0.7 - - + -
315A LEU 3.2 6.1 + - - +
316A ILE* 4.1 7.6 - - - +
318A HIS* 1.3 77.2 - - - +
320A VAL* 1.3 57.0 + - - +
322A HIS* 3.6 0.7 + - - +
323A LEU* 3.0 36.7 + - - +
343A LEU* 3.8 22.2 - - + -
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Residues in contact with VAL 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 ILE* 3.2 28.1 + - + +
317A GLY* 3.6 5.4 - - - +
318A HIS 3.0 1.4 - - - -
319A ALA* 1.3 75.2 - - - +
321A ALA* 1.3 68.9 + - - +
323A LEU 3.3 0.7 + - - -
324A LYS* 2.9 37.2 + - - +
340A LEU* 3.9 19.8 - - + +
343A LEU* 4.2 17.5 - - + -
344A HIS* 3.5 39.7 - - + +
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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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317A GLY 3.0 14.7 + - - +
318A HIS* 3.7 8.5 - - - +
320A VAL* 1.3 79.2 - - - +
322A HIS* 1.3 65.5 + - + +
324A LYS* 3.4 10.0 - - - +
325A LYS* 3.3 36.1 + - - +
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Residues in contact with HIS 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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274A LEU* 4.2 10.7 - - + +
284A HIS* 2.9 65.4 + + - +
287A ILE* 3.2 29.4 - - + +
288A GLY* 3.8 9.6 - - - -
291A TYR* 3.8 22.5 - + - -
318A HIS* 3.1 30.6 + + - +
321A ALA* 1.3 79.3 - - + +
323A LEU* 1.3 65.6 + - - +
325A LYS* 3.2 10.8 + - + +
326A ALA 3.4 8.0 + - - -
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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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285A CYS* 3.8 31.0 - - - +
288A GLY* 3.9 16.8 - - - +
289A CYS* 4.2 8.3 - - - +
292A ARG* 5.3 0.4 - - + -
319A ALA 3.0 22.5 + - - +
322A HIS* 1.3 72.1 - - - +
324A LYS* 1.3 60.8 + - - +
326A ALA* 3.2 5.2 + - + +
327A ASP* 2.9 30.0 + - - +
336A VAL* 3.4 27.5 - - + +
339A ILE* 3.7 28.7 - - + -
340A LEU* 3.9 20.4 - - + -
343A LEU* 3.7 15.3 - - + -
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Residues in contact with LYS 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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320A VAL* 2.9 36.6 + - + +
321A ALA* 3.4 9.0 - - - +
323A LEU* 1.3 76.6 - - - +
325A LYS* 1.3 62.1 + - + +
327A ASP* 3.9 4.1 - - - +
328A GLU* 3.0 45.2 + - - +
340A LEU* 4.2 9.1 - - + +
344A HIS* 4.5 8.3 + - - -
352A GLU* 5.7 3.6 - - - +
356A TYR* 3.1 31.2 - - - +
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Residues in contact with LYS 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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279A ASN* 6.1 0.4 - - - +
281A ALA* 5.2 0.8 - - - +
284A HIS* 3.7 38.5 + - + +
321A ALA* 3.3 25.5 + - - +
322A HIS* 3.2 10.1 + - - +
324A LYS* 1.3 78.0 - - + +
326A ALA* 1.3 57.9 + - - +
328A GLU* 3.5 13.7 + - - +
329A ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 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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281A ALA* 4.1 8.7 - - - +
284A HIS* 4.5 0.8 - - - +
285A CYS* 4.0 37.5 - - + +
322A HIS 3.4 4.4 + - - +
323A LEU* 3.2 10.2 + - - +
325A LYS* 1.3 77.2 - - - +
327A ASP* 1.3 64.9 + - - +
329A ALA* 3.1 14.1 + - - +
330A ASN 3.2 10.2 + - - -
334A PHE* 3.4 28.7 - - + +
336A VAL* 5.0 2.2 - - + -
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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
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323A LEU 2.9 17.2 + - - +
324A LYS* 3.9 7.7 - - - +
326A ALA* 1.3 75.5 - - - +
328A GLU* 1.3 68.2 + - - +
330A ASN 4.9 0.2 - - - -
331A ASP* 3.4 28.6 + - - +
334A PHE 4.3 8.4 - - - +
336A VAL* 3.5 18.9 - - + +
337A CYS* 3.8 12.5 - - - -
340A LEU* 4.5 6.0 - - + +
356A TYR* 4.5 9.6 + - - -
359A LYS* 3.1 33.5 + - - -
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Residues in contact with GLU 328 (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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324A LYS* 3.0 42.7 + - + +
325A LYS* 3.8 15.4 - - - +
327A ASP* 1.3 81.7 - - - +
329A ALA* 1.3 65.9 + - - +
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Residues in contact with ALA 329 (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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36A ASP* 4.0 9.0 - - - +
40A TYR* 4.1 19.3 - - + +
281A ALA* 3.7 26.2 - - + -
325A LYS 3.0 15.0 + - - +
326A ALA 3.1 9.4 + - - +
328A GLU* 1.3 81.6 - - - +
330A ASN* 1.3 63.7 + - - +
334A PHE* 4.6 0.9 - - + -
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Residues in contact with ASN 330 (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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32A ASP* 4.3 2.0 + - - +
33A ASP* 3.3 20.5 + - - +
36A ASP* 3.0 24.9 + - + +
40A TYR* 5.8 0.7 - - + -
326A ALA 3.2 2.4 + - - -
327A ASP 3.8 2.9 - - - -
329A ALA* 1.3 83.6 + - + +
331A ASP* 1.3 54.4 + - - +
332A ASN* 3.0 14.9 + - - +
333A LEU* 3.0 45.3 + - + +
334A PHE* 2.8 40.9 + - + +
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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