Contacts of the helix formed by residues 343 - 361 (chain A) in PDB entry 1W3U
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN 5.9 0.9 - - - +
14A ALA* 5.5 2.9 - - + -
271A LYS* 4.4 0.7 - - - -
341A ALA 3.2 11.2 - - - +
342A VAL* 1.3 89.0 - - + +
344A TYR* 1.3 65.9 + - - +
345A GLU* 4.0 18.8 - - + +
346A SER* 3.0 33.9 + - - +
347A CYS* 3.4 9.7 + - - -
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Residues in contact with TYR 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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267A ALA 5.4 0.2 - - - -
270A LYS* 3.7 57.2 - - + +
271A LYS* 3.8 30.9 - - + +
274A LEU* 3.7 33.5 - - + +
342A VAL 3.7 1.2 + - - -
343A PRO* 1.3 70.2 - - - +
345A GLU* 1.3 67.3 + - - +
347A CYS* 2.9 7.6 + - + +
348A GLU* 2.8 61.2 + - + +
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Residues in contact with GLU 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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6A TYR* 4.4 6.2 - - + -
343A PRO* 3.1 13.2 - - + +
344A TYR* 1.3 88.2 + - - +
346A SER* 1.3 62.4 + - - +
348A GLU* 3.6 23.3 - - - +
349A ALA* 3.0 23.0 + - - +
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Residues in contact with SER 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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5A ALA 4.6 2.4 + - - -
6A TYR* 3.7 28.8 - - - -
7A ASN 4.5 3.4 + - - -
8A PHE* 3.3 29.5 - - - -
342A VAL* 4.1 9.9 - - - -
343A PRO* 3.0 26.0 + - - +
345A GLU* 1.3 78.5 - - - +
347A CYS* 1.3 58.3 + - - +
349A ALA* 3.3 3.6 + - - +
350A LEU 2.8 23.2 + - - -
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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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8A PHE* 4.1 5.6 - - - -
271A LYS* 3.8 32.1 - - + +
274A LEU* 3.9 12.1 - - + -
275A ILE* 3.9 13.9 - - + -
338A ILE* 3.7 29.2 - - - -
342A VAL* 4.2 7.6 - - - -
343A PRO 3.8 7.6 - - - -
344A TYR* 2.9 10.9 + - - +
346A SER* 1.3 74.3 - - - +
348A GLU* 1.3 60.4 + - - +
350A LEU* 3.2 4.2 + - - +
351A VAL* 2.9 33.4 + - - +
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Residues in contact with GLU 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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274A LEU* 3.8 11.6 - - + +
344A TYR* 2.8 54.9 + - + +
345A GLU* 3.6 28.5 - - - +
347A CYS* 1.3 76.8 - - - +
349A ALA* 1.3 62.6 + - - +
351A VAL* 3.3 4.3 + - - +
352A GLN* 2.9 42.0 + - - +
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Residues in contact with ALA 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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6A TYR* 3.6 36.3 - - + +
322A PHE* 3.3 13.3 - - + -
345A GLU 3.0 14.7 + - - +
346A SER 3.4 8.7 - - - +
348A GLU* 1.3 77.4 - - - +
350A LEU* 1.3 57.8 + - - +
352A GLN* 3.4 14.0 + - - +
353A PHE* 2.9 24.4 + - - +
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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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8A PHE* 3.7 18.6 - - + -
275A ILE* 4.0 17.3 - - + -
302A PHE* 5.4 2.9 - - + -
313A PHE* 4.5 7.9 - - + -
322A PHE* 3.5 12.1 - - + -
325A LEU* 3.7 29.8 - - + -
336A ALA* 3.6 31.0 - - + -
346A SER 2.8 14.2 + - - +
347A CYS 3.2 7.6 + - - +
349A ALA* 1.3 76.7 - - - +
351A VAL* 1.3 57.8 + - - +
353A PHE* 3.2 5.3 + - + +
354A MET* 2.7 51.8 + - + +
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Residues in contact with VAL 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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274A LEU* 3.7 44.2 - - + +
275A ILE* 3.9 21.5 - - + -
278A ALA* 3.9 15.6 - - + +
347A CYS 2.9 22.1 + - - +
348A GLU* 3.4 10.3 - - - +
350A LEU* 1.3 69.1 - - - +
352A GLN* 1.3 74.9 + - + +
354A MET* 3.1 11.9 + - - +
355A GLU* 3.0 23.2 + - - +
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Residues in contact with GLN 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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348A GLU* 2.9 36.6 + - - +
349A ALA* 3.6 12.6 - - - +
351A VAL* 1.3 80.9 - - + +
353A PHE* 1.3 62.3 + - - +
355A GLU* 3.2 5.8 + - - +
356A HIS* 2.9 47.2 + - + +
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Residues in contact with PHE 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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313A PHE* 3.6 40.6 - + - -
316A ALA* 3.8 13.9 - - + -
317A SER* 3.4 38.6 - - - -
320A GLU* 3.5 37.0 - - - +
322A PHE* 3.7 20.0 - + + -
349A ALA 2.9 18.7 + - - +
350A LEU* 3.5 7.9 - - + +
352A GLN* 1.3 75.8 - - - +
354A MET* 1.3 60.2 + - - +
356A HIS* 3.7 11.4 + - + -
357A PHE* 2.8 44.9 + + + +
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Residues in contact with MET 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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275A ILE* 4.6 6.1 - - + +
278A ALA* 4.1 18.8 - - + -
279A ILE* 4.0 21.3 - - + -
286A TYR* 2.6 56.8 + - + +
302A PHE* 4.1 16.4 - - + -
313A PHE* 3.8 22.4 - - + -
350A LEU* 2.7 40.6 + - + +
351A VAL* 3.1 16.4 + - - +
353A PHE* 1.3 75.4 - - - +
355A GLU* 1.3 57.1 + - - +
358A LYS* 3.0 19.2 + - - +
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Residues in contact with GLU 355 (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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286A TYR* 5.5 0.4 - - - -
351A VAL 3.0 12.0 + - - +
352A GLN* 3.4 7.9 - - - +
354A MET* 1.3 76.0 - - - +
356A HIS* 1.3 82.0 + - + +
358A LYS* 3.3 15.9 + - - +
359A ARG* 3.0 62.1 + - + +
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Residues in contact with HIS 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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320A GLU* 5.4 6.9 + - - +
352A GLN* 2.9 38.9 + - + +
353A PHE* 3.7 11.4 - - + +
355A GLU* 1.3 88.8 - - + +
357A PHE* 1.3 63.3 + - - +
359A ARG* 3.4 4.3 + - - +
360A SER* 2.9 26.7 + - - -
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Residues in contact with PHE 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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285A PHE* 4.0 7.2 - + - -
286A TYR* 3.7 16.2 - - - +
304A LEU* 3.6 23.8 - - + -
309A LEU* 3.8 7.0 - - + -
312A GLU* 3.7 10.3 - - + -
313A PHE* 3.5 38.4 - + - -
316A ALA* 4.4 4.3 - - + -
353A PHE* 2.8 47.0 + + + +
356A HIS* 1.3 73.9 - - - +
358A LYS* 1.3 66.5 + - - +
360A SER* 2.9 19.4 + - - -
361A ARG* 3.2 64.0 + - + -
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Residues in contact with LYS 358 (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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281A GLN 5.4 2.0 + - - -
282A SER* 3.9 27.5 - - - +
285A PHE* 3.7 53.2 - - + -
286A TYR* 4.2 3.4 - - + +
354A MET 3.0 18.6 + - - +
355A GLU* 3.6 25.5 + - - +
356A HIS 3.3 0.2 - - - -
357A PHE* 1.3 80.1 - - - +
359A ARG* 1.3 71.7 + - - +
361A ARG* 3.3 4.2 + - - +
362A GLY* 3.0 22.3 + - - -
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Residues in contact with ARG 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 GLU* 3.0 43.8 + - - +
356A HIS* 4.0 4.9 - - - +
358A LYS* 1.3 89.2 - - + +
360A SER* 1.3 57.5 + - - +
361A ARG 3.1 5.6 - - - -
362A GLY* 3.3 19.2 + - - +
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Residues in contact with SER 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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356A HIS 2.9 17.1 + - - -
357A PHE* 2.9 19.8 + - - -
359A ARG* 1.3 76.9 - - - +
361A ARG* 1.3 82.8 + - - +
362A GLY* 3.5 1.2 - - - +
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Residues in contact with ARG 361 (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 PHE* 4.2 12.3 - - + -
309A LEU* 3.6 25.8 - - + -
312A GLU* 2.9 32.1 + - - +
316A ALA* 5.3 5.9 - - - +
357A PHE* 3.2 52.1 + - + +
358A LYS 3.6 5.6 - - - +
359A ARG 3.1 0.2 - - - -
360A SER* 1.3 100.2 + - - +
362A GLY* 1.3 67.0 + - - +
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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