Contacts of the helix formed by residues 307 - 316 (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 LYS 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A ASN* 4.5 8.1 - - - +
271A GLN* 5.9 1.3 - - + -
304A ALA* 3.1 9.1 + - + +
305A ARG 3.4 1.2 + - - -
306A PHE* 1.3 81.5 - - - +
308A ALA* 1.3 66.0 + - - +
309A GLY 3.2 2.5 - - - -
310A GLN* 2.8 35.3 + - + +
311A VAL* 3.3 8.3 + - - +
380A PHE* 3.8 3.3 - - - -
391A HIS* 3.5 48.0 - - + +
392A ALA 3.1 26.5 - - - +
393A PHE* 3.7 4.0 - - - -
1B GLC 2.6 49.5 + - - +
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Residues in contact with ALA 308 (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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304A ALA 2.9 11.3 + - - +
305A ARG 4.7 0.2 + - - -
307A LYS* 1.3 76.0 - - - +
309A GLY* 1.3 61.8 + - - +
311A VAL* 3.1 8.3 + - - +
312A ILE* 3.0 32.7 + - + +
383A ALA* 4.7 6.1 - - + -
388A LEU* 3.2 40.8 - - + +
390A VAL* 3.5 19.2 + - + +
417A PHE* 4.6 2.4 - - + -
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Residues in contact with GLY 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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305A ARG 5.2 0.8 + - - -
307A LYS 3.2 1.0 - - - -
308A ALA* 1.3 78.2 - - - +
310A GLN* 1.3 59.8 + - - +
312A ILE* 3.5 5.0 + - - +
313A GLY* 3.2 17.2 + - - -
376A THR* 4.9 3.3 - - - +
379A ALA* 3.6 31.8 + - - +
380A PHE* 3.4 32.0 + - - +
383A ALA* 5.8 0.2 - - - +
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Residues in contact with GLN 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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231A GLU* 4.3 2.9 - - - +
232A ARG* 3.9 14.6 - - - +
307A LYS* 2.8 39.9 + - + +
309A GLY* 1.3 74.5 - - - +
311A VAL* 1.3 67.1 + - - +
313A GLY* 3.3 2.0 + - - +
314A SER* 3.2 21.7 + - - -
352A GLY 3.1 25.7 + - - -
354A THR* 3.8 9.3 - - - +
380A PHE* 3.3 19.8 - - + -
392A ALA 4.5 0.9 - - - +
393A PHE* 3.5 8.2 - - - -
394A GLY 5.4 0.3 + - - -
1B GLC 3.8 2.5 - - - +
2B GLC 3.3 36.2 + - - +
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Residues in contact with VAL 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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307A LYS* 3.3 17.5 - - - +
308A ALA* 3.1 12.1 + - - +
310A GLN* 1.3 75.8 - - - +
312A ILE* 1.3 65.6 + - - +
314A SER* 3.6 5.7 + - - +
315A THR* 2.7 38.0 + - - +
390A VAL* 4.3 5.2 - - + +
392A ALA* 3.1 38.8 - - + +
394A GLY 5.2 6.5 - - - +
398A LEU* 4.5 19.3 - - + -
417A PHE* 3.7 24.9 - - + -
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Residues in contact with ILE 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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308A ALA* 3.0 16.5 + - + +
309A GLY* 3.7 7.2 - - - +
310A GLN 3.3 0.2 - - - -
311A VAL* 1.3 75.8 - - - +
313A GLY* 1.3 58.3 + - - +
316A ALA* 3.1 8.3 + - - +
317A ALA* 2.9 24.4 + - + -
379A ALA* 3.9 28.0 - - + +
388A LEU* 4.2 15.0 - - + -
417A PHE* 3.8 22.4 - - + -
420A VAL* 3.6 28.5 - - + -
421A SER* 4.5 13.5 - - - +
424A PHE* 4.1 31.2 - - + -
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Residues in contact with GLY 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 GLY 3.2 14.3 + - - -
310A GLN* 3.3 4.0 + - - -
311A VAL 3.2 0.8 - - - -
312A ILE* 1.3 78.7 - - - +
314A SER* 1.3 61.0 + - - +
315A THR 3.3 0.2 + - - -
317A ALA* 3.3 14.2 + - - -
318A LEU* 2.6 35.4 + - - +
354A THR* 5.0 3.6 - - - -
372A TYR* 5.7 3.4 - - - -
376A THR* 5.3 9.2 - - - -
379A ALA* 5.6 0.4 - - - +
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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 GLN* 3.2 16.9 + - - -
311A VAL* 3.6 7.8 + - - +
313A GLY* 1.3 75.0 - - - +
315A THR* 1.3 62.5 + - - +
319A MSE 3.5 11.1 - - - +
348A VAL* 3.5 30.9 - - - +
349A PHE* 3.4 22.6 + - - -
352A GLY* 3.7 27.4 + - - -
354A THR* 3.8 7.8 - - - +
394A GLY* 4.8 5.9 + - - -
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Residues in contact with THR 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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311A VAL* 2.7 34.7 + - - +
312A ILE* 4.4 1.6 - - - -
314A SER* 1.3 82.7 + - - +
316A ALA* 1.3 60.4 + - + +
319A MSE 3.1 15.8 - - - +
349A PHE* 3.3 36.7 + - + +
394A GLY 5.5 0.2 - - - -
395A PHE* 4.3 17.6 + - + -
398A LEU* 4.7 3.5 - - - +
417A PHE* 4.3 16.7 - - + -
421A SER* 4.8 8.1 - - - +
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Residues in contact with ALA 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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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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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