Contacts of the helix formed by residues 316 - 328 (chain A) in PDB entry 5IWS
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 ALA 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A ILE 3.1 5.2 + - - +
313A GLY 3.6 0.6 + - - -
315A THR* 1.3 81.7 - - + +
317A ALA* 1.3 67.1 + - - +
318A LEU 3.2 2.0 - - - -
319A MSE 3.0 17.3 + - - +
320A GLY 3.0 11.4 + - - -
421A SER* 3.2 46.9 - - - +
424A PHE* 5.3 0.2 - - + -
425A PHE* 3.3 19.3 - - + -
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Residues in contact with ALA 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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312A ILE* 2.9 22.3 + - + +
313A GLY* 3.6 11.4 - - - -
316A ALA* 1.3 74.4 - - - +
318A LEU* 1.3 59.7 + - - +
321A ILE* 3.4 8.1 + - - +
372A TYR* 5.7 0.9 - - + -
376A THR* 5.4 7.2 - - + -
379A ALA* 5.9 2.0 - - + -
424A PHE* 4.0 27.3 - - + +
425A PHE 4.6 0.2 - - - +
428A ASN* 2.8 45.0 + - - +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLY* 2.6 24.7 + - - +
314A SER* 4.6 0.2 - - - -
317A ALA* 1.3 71.2 - - - +
319A MSE 1.3 65.1 + - + +
320A GLY 3.4 0.2 - - - -
321A ILE* 3.4 14.1 + - + +
322A ALA* 3.0 26.7 + - - +
348A VAL* 3.6 22.7 - - + -
354A THR* 3.6 36.3 - - + +
357A ILE* 3.6 26.7 - - + +
358A GLU* 4.1 5.6 - - + -
361A PHE* 4.3 3.4 - - + -
372A TYR* 3.6 33.8 - - + +
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Residues in contact with MSE 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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314A SER 3.5 17.5 - - - +
315A THR 3.1 28.9 - - - +
316A ALA 3.0 8.1 + - - +
318A LEU* 1.3 78.0 - - + +
320A GLY* 1.3 59.6 + - - +
322A ALA* 3.2 4.1 + - - +
323A PHE* 2.9 29.6 + - - +
345A ALA* 3.5 39.5 - - - +
348A VAL* 3.8 10.5 - - + -
349A PHE* 4.0 13.7 - - + -
357A ILE* 3.6 22.4 - - + -
425A PHE* 3.5 17.3 - - + -
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Residues in contact with GLY 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 ALA 3.0 11.7 + - - -
317A ALA 3.8 2.0 + - - -
318A LEU 3.4 0.2 - - - -
319A MSE 1.3 78.4 - - - +
321A ILE* 1.3 55.3 + - - +
323A PHE* 4.4 1.1 - - - -
324A ALA* 2.8 30.8 + - - +
425A PHE* 3.3 34.4 - - - -
429A PHE* 3.5 16.7 - - - -
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Residues in contact with ILE 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 ALA 3.4 18.1 + - - +
318A LEU* 3.4 18.3 + - + +
319A MSE 3.2 0.4 - - - -
320A GLY* 1.3 74.5 - - - +
322A ALA* 1.3 65.0 + - - +
324A ALA* 3.9 5.4 - - - +
325A MSE 3.0 29.7 + - - +
357A ILE* 4.6 1.8 - - + -
361A PHE* 3.7 24.0 - - + -
372A TYR* 3.5 33.7 - - + -
428A ASN* 3.9 7.6 - - + +
432A PHE* 3.5 50.0 - - + -
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Residues in contact with ALA 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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318A LEU 3.0 16.7 + - - +
319A MSE 3.2 6.5 + - - +
321A ILE* 1.3 76.7 - - - +
323A PHE* 1.3 57.9 + - - +
325A MSE 4.8 2.2 - - - -
326A PHE* 3.1 22.5 + - - +
341A PHE* 3.4 25.6 - - + +
345A ALA* 4.2 15.9 - - + -
357A ILE* 3.6 28.0 - - + -
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Residues in contact with PHE 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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319A MSE 2.9 16.6 + - - +
320A GLY* 3.9 5.8 - - - +
322A ALA* 1.3 75.0 - - - +
324A ALA* 1.3 60.3 + - - +
326A PHE* 4.3 25.4 - + + -
327A ARG* 2.9 50.8 + - - +
425A PHE* 4.5 17.7 - + + -
429A PHE* 3.4 32.8 - + + -
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Residues in contact with ALA 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 GLY 2.8 19.0 + - - +
321A ILE 3.4 3.6 + - - +
323A PHE* 1.3 74.6 - - - +
325A MSE 1.3 61.9 + - - +
327A ARG* 3.5 0.7 + - - +
328A ASN* 2.3 38.3 + - - +
429A PHE* 3.5 34.2 - - + +
432A PHE* 3.9 11.0 - - + -
433A ASN* 3.7 15.3 - - - +
436A ILE* 4.5 1.3 - - + -
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Residues in contact with MSE 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 ILE* 3.0 27.1 + - + +
322A ALA* 4.6 0.7 - - - -
324A ALA* 1.3 73.8 - - - +
326A PHE* 1.3 66.5 + - - +
328A ASN* 3.2 5.0 + - - +
329A VAL* 3.2 22.5 + - - +
341A PHE* 3.4 26.7 - - + -
357A ILE* 4.8 4.3 - - - +
360A MSE 3.5 28.3 - - + +
361A PHE* 3.8 36.8 - - - -
368A LEU* 5.8 0.4 - - + -
432A PHE* 5.5 1.1 - - + -
436A ILE* 3.7 24.7 - - + -
443A THR* 3.8 14.3 + - + -
444A PRO* 3.5 22.4 - - + -
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Residues in contact with PHE 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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322A ALA 3.1 19.7 + - - +
323A PHE* 4.0 25.4 - + + +
324A ALA 3.3 0.2 - - - -
325A MSE 1.3 76.0 - - - +
327A ARG* 1.3 80.9 + - - +
329A VAL* 3.2 24.1 + - + +
334A ARG* 3.4 37.2 + - + -
337A TYR 4.5 0.9 - - - -
338A LYS* 3.6 43.3 - - + -
341A PHE* 3.7 31.5 - + + -
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Residues in contact with ARG 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 PHE* 2.9 44.9 + - - +
324A ALA 3.8 5.4 - - - +
325A MSE 3.3 0.2 - - - -
326A PHE* 1.3 86.7 - - - +
328A ASN* 1.3 59.8 + - - +
329A VAL 3.4 0.2 - - - -
334A ARG* 2.8 60.7 + - - +
429A PHE* 4.4 17.0 - - + -
433A ASN* 4.8 6.5 - - - +
437A LYS* 6.0 1.6 - - - +
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Residues in contact with ASN 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 ALA 2.3 36.0 + - - +
325A MSE 3.2 5.8 + - - +
326A PHE 3.1 1.0 - - - -
327A ARG* 1.3 75.6 - - - +
329A VAL* 1.3 65.9 + - - +
330A ASP* 3.6 1.7 + - - +
433A ASN* 3.3 27.5 + - - +
436A ILE* 3.8 19.7 - - + +
437A LYS* 3.2 38.0 - - - +
446A ARG* 2.8 42.0 + - - +
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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