Contacts of the helix formed by residues 340 - 360 (chain A) in PDB entry 4N4H
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A TRP* 4.2 8.7 + - - -
338A LYS* 2.8 13.3 + - - -
339A ARG* 1.3 77.7 - - - +
341A MET* 1.3 64.1 + - - +
342A GLY* 3.7 3.8 + - - -
343A TRP* 3.2 25.9 + - - +
344A LYS* 3.3 12.5 + - - +
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Residues in contact with MET 341 (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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340A SER* 1.3 73.4 - - - +
342A GLY* 1.3 62.6 + - - +
344A LYS* 3.2 17.1 + - - +
345A LYS* 3.2 13.9 + - - +
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Residues in contact with GLY 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TRP* 3.4 18.9 - - - -
312A GLY* 4.7 2.4 - - - -
313A HIS* 4.9 14.4 + - - -
340A SER* 3.3 5.4 + - - -
341A MET* 1.3 79.8 - - - +
343A TRP* 1.3 55.9 + - - +
345A LYS* 3.5 9.0 + - - +
346A ALA* 3.0 22.3 + - - +
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Residues in contact with TRP 343 (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 TRP* 4.6 1.5 - + - -
293A PHE 3.1 20.7 + - - -
294A TRP* 3.5 38.2 - + + -
295A PRO* 4.4 5.6 - - + +
332A VAL* 3.4 35.9 - - + -
337A VAL* 3.7 17.4 - - + +
338A LYS 3.7 13.9 - - - +
339A ARG* 3.3 51.8 - - + -
340A SER* 3.2 22.5 + - - +
341A MET 3.2 0.6 - - - -
342A GLY* 1.3 75.0 - - - +
344A LYS* 1.3 77.4 + - + +
346A ALA* 3.2 3.7 + - - +
347A CYS* 2.9 50.5 + - - -
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Residues in contact with LYS 344 (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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339A ARG* 5.7 4.5 - - + +
340A SER 3.3 7.4 + - - +
341A MET* 3.2 12.4 + - - +
343A TRP* 1.3 94.3 - - + +
345A LYS* 1.3 59.7 + - - +
347A CYS* 3.2 6.5 + - + +
348A ASP* 2.9 58.5 + - - +
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Residues in contact with LYS 345 (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 ASN* 5.5 4.8 + - - -
312A GLY* 4.4 8.7 - - - -
313A HIS* 3.6 43.5 - - + +
341A MET 3.2 9.7 + - - +
342A GLY 3.7 7.4 - - - +
343A TRP 3.3 0.2 - - - -
344A LYS* 1.3 77.9 - - - +
346A ALA* 1.3 56.6 + - - +
348A ASP* 3.3 12.0 + - + +
349A GLU* 2.9 47.0 + - - +
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Residues in contact with ALA 346 (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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294A TRP* 3.5 17.0 - - + -
295A PRO* 4.1 10.5 - - + -
311A PHE* 3.4 30.8 - - - +
312A GLY* 3.7 11.7 - - - +
342A GLY 3.0 14.9 + - - +
343A TRP* 3.2 9.6 + - - +
345A LYS* 1.3 77.5 - - - +
347A CYS* 1.3 57.7 + - - +
349A GLU 3.3 0.9 + - - -
350A LEU* 2.9 27.9 + - - +
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Residues in contact with CYS 347 (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 TRP* 4.3 19.5 - - + -
295A PRO* 4.4 4.0 - - - -
332A VAL* 5.2 0.4 - - - -
343A TRP* 2.9 61.5 + - + +
344A LYS* 3.7 9.2 - - + +
346A ALA* 1.3 74.3 - - - +
348A ASP* 1.3 63.0 + - - +
350A LEU* 3.3 11.0 + - + +
351A GLU* 3.0 28.2 + - - +
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Residues in contact with ASP 348 (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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344A LYS* 2.9 48.4 + - - +
345A LYS* 3.6 13.6 - - + +
347A CYS* 1.3 75.9 - - - +
349A GLU* 1.3 63.2 + - - +
351A GLU* 3.4 6.3 + - - +
352A LEU* 3.1 23.7 + - - +
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Residues in contact with GLU 349 (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 ASN* 5.7 2.8 - - - -
272A TRP* 5.8 0.3 + - - -
273A PHE* 3.6 17.4 + - - +
274A CYS* 3.5 22.0 - - - -
311A PHE* 3.4 11.1 - - + -
312A GLY* 2.6 33.8 + - - +
315A HIS* 2.8 29.3 + - - -
345A LYS* 2.9 34.9 + - - +
346A ALA 3.7 4.3 - - - +
348A ASP* 1.3 73.4 - - - +
350A LEU* 1.3 65.6 + - - +
352A LEU* 3.4 2.6 + - - -
353A HIS* 3.0 22.9 + - - +
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Residues in contact with LEU 350 (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 LEU* 4.4 7.9 - - + -
285A TRP* 4.1 14.1 - - + -
295A PRO* 3.7 17.7 - - + -
311A PHE* 3.7 33.3 - - + -
328A ILE* 3.7 35.2 - - + -
346A ALA 2.9 15.1 + - - +
347A CYS* 3.4 13.0 - - + +
348A ASP 3.2 0.2 - - - -
349A GLU* 1.3 76.2 - - - +
351A GLU* 1.3 57.6 + - - +
353A HIS* 3.1 4.2 + - - +
354A GLN* 2.9 54.5 + - + +
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Residues in contact with GLU 351 (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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347A CYS 3.0 16.1 + - - +
348A ASP* 3.9 6.1 - - - +
350A LEU* 1.3 77.3 - - - +
352A LEU* 1.3 58.8 + - - +
354A GLN* 3.3 17.8 + - - +
355A ARG* 3.0 22.2 + - + +
358A ARG* 3.1 26.9 + - - -
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Residues in contact with LEU 352 (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 ASN* 3.6 38.4 - - + +
274A CYS* 3.8 13.2 - - - -
348A ASP 3.1 17.2 + - - +
349A GLU* 3.7 6.3 - - - +
351A GLU* 1.3 76.1 - - - +
353A HIS* 1.3 57.1 + - - +
355A ARG* 3.4 25.6 + - - +
356A PHE* 3.0 61.1 + - + -
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Residues in contact with HIS 353 (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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273A PHE 4.1 1.4 + - - -
274A CYS* 2.6 41.2 + - - +
275A TYR 4.3 0.7 - - - -
276A PRO* 4.0 22.0 - - + -
281A HIS* 5.2 6.3 + + + +
283A LEU* 3.7 40.3 - - + +
297A LYS* 4.1 14.8 - - - -
311A PHE* 3.8 19.7 - + + -
349A GLU 3.0 13.7 + - - +
350A LEU 3.1 8.9 + - - +
352A LEU* 1.3 74.8 - - - +
354A GLN* 1.3 59.0 + - - +
356A PHE* 3.4 1.7 + - - +
357A LEU* 3.0 43.2 + - + +
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Residues in contact with GLN 354 (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 LEU* 4.1 14.7 - - + +
328A ILE* 3.8 27.0 - - - +
350A LEU* 2.9 46.3 + - + +
351A GLU* 3.3 21.2 + - - +
353A HIS* 1.3 76.5 - - - +
355A ARG* 1.3 61.2 + - - +
357A LEU* 3.4 9.8 + - + +
358A ARG* 3.1 47.3 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A GLU* 3.0 15.2 + - + +
352A LEU* 3.5 31.2 - - - +
353A HIS 3.2 0.2 - - - -
354A GLN* 1.3 74.5 - - - +
356A PHE* 1.3 61.5 + - - +
358A ARG* 3.1 22.0 + - - +
359A GLU* 2.8 62.9 + - + +
361A ARG* 3.7 16.3 - - - +
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Residues in contact with PHE 356 (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 ASN* 4.3 11.2 - - + -
274A CYS* 3.7 44.0 - - + +
275A TYR* 4.0 26.2 - + - -
276A PRO* 4.1 9.9 - - + +
352A LEU* 3.0 46.5 + - + +
353A HIS 3.7 0.4 - - - +
355A ARG* 1.3 79.8 - - + +
357A LEU* 1.3 57.0 + - - +
359A GLU* 3.7 8.3 - - - -
360A GLY* 3.0 7.6 + - - -
361A ARG* 3.0 81.3 + - - +
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Residues in contact with LEU 357 (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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276A PRO* 3.7 25.9 - - + +
280A ASN* 3.5 39.7 - - + +
281A HIS 5.5 2.0 - - - +
283A LEU* 4.4 14.6 - - + -
353A HIS* 3.0 33.2 + - + +
354A GLN* 3.4 12.8 - - + +
355A ARG 3.1 0.2 - - - -
356A PHE* 1.3 77.2 - - - +
358A ARG* 1.3 62.2 + - + +
360A GLY* 3.3 11.1 + - - -
362A PHE* 6.2 0.9 - - + -
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Residues in contact with ARG 358 (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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351A GLU* 3.1 24.4 + - - -
354A GLN* 3.1 37.7 + - - +
355A ARG* 3.1 21.6 + - - +
357A LEU* 1.3 78.9 - - + +
359A GLU* 1.3 63.2 + - + +
360A GLY* 3.3 0.9 + - - -
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Residues in contact with GLU 359 (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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355A ARG* 2.8 55.8 + - + +
356A PHE* 3.7 10.5 - - - +
357A LEU 3.3 0.2 - - - -
358A ARG* 1.3 77.6 - - + +
360A GLY* 1.3 61.2 + - - +
361A ARG* 2.9 40.2 + - + +
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Residues in contact with GLY 360 (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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276A PRO* 5.4 0.7 - - - -
356A PHE 3.0 6.0 + - - -
357A LEU 3.3 7.3 + - - -
358A ARG 3.2 5.2 + - - -
359A GLU* 1.3 80.0 - - - +
361A ARG* 1.3 59.3 + - - +
362A PHE* 3.2 34.5 + - - -
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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