Contacts of the helix formed by residues 300 - 315 (chain A) in PDB entry 4B8Z
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 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A PHE 3.6 7.1 - - - +
299A THR* 1.4 89.4 - - + +
301A PHE* 1.3 65.4 + - - +
302A LYS* 3.3 2.9 - - + +
303A GLN* 3.0 29.2 + - + +
304A ALA* 3.0 10.6 + - - +
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Residues in contact with PHE 301 (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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174A PHE* 4.5 6.9 - - + -
217A PHE* 6.3 2.7 - - + -
258A ALA* 5.9 0.4 - - - -
299A THR 3.3 5.8 + - - -
300A PRO* 1.3 69.6 - - - +
302A LYS* 1.3 54.0 + - + +
304A ALA* 3.3 6.2 + - - +
305A VAL* 2.9 44.0 + - + +
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Residues in contact with LYS 302 (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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258A ALA* 4.8 21.1 - - + +
261A GLU* 6.2 3.6 - - + -
262A ALA* 5.2 1.6 - - - +
300A PRO* 3.3 4.1 - - + +
301A PHE* 1.3 78.1 - - + +
303A GLN* 1.4 56.2 + - - +
305A VAL* 3.9 6.3 - - - +
306A LYS* 3.1 29.3 + - - +
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Residues in contact with GLN 303 (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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299A THR* 4.4 3.4 - - + -
300A PRO* 3.0 29.2 + - + +
302A LYS* 1.4 75.7 - - - +
304A ALA* 1.3 57.7 + - - +
306A LYS* 3.6 6.4 + - - +
307A GLU* 3.1 43.6 + - - +
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Residues in contact with ALA 304 (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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174A PHE* 3.6 24.0 - - + -
219A TYR* 3.7 29.7 - - + -
299A THR* 4.0 11.8 - - + +
300A PRO 3.0 11.9 + - - +
301A PHE* 3.7 5.6 - - - +
303A GLN* 1.3 74.6 - - - +
305A VAL* 1.4 54.7 + - - +
307A GLU* 3.6 6.8 + - - +
308A THR* 2.7 36.2 + - - -
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Residues in contact with VAL 305 (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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174A PHE* 4.0 20.4 - - + -
188A LEU* 6.2 3.6 - - + -
255A ALA 5.6 0.4 - - - +
258A ALA* 3.6 40.8 - - + +
259A VAL* 4.0 13.2 - - + -
262A ALA* 4.0 1.3 - - + -
301A PHE* 2.9 24.4 + - + +
302A LYS* 3.9 5.8 - - - +
304A ALA* 1.4 71.7 - - - +
306A LYS* 1.4 55.4 + - - +
308A THR* 3.1 5.3 + - - -
309A CYS* 2.8 52.2 + - - -
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Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLU 4.2 5.5 + - - -
262A ALA* 3.5 44.8 + - + +
264A ASP* 5.8 2.4 - - - +
302A LYS 3.1 19.0 + - - +
303A GLN* 3.7 7.4 - - - +
304A ALA 3.4 0.2 - - - -
305A VAL* 1.4 76.0 - - - +
307A GLU* 1.4 56.1 + - - +
309A CYS* 3.4 1.7 + - - +
310A ALA* 2.9 33.4 + - + +
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Residues in contact with GLU 307 (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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176A PRO* 5.4 1.8 - - - +
219A TYR* 3.4 31.3 + - - +
299A THR* 4.6 8.0 - - - +
303A GLN* 3.1 32.3 + - - +
304A ALA* 3.8 7.6 - - - +
305A VAL 3.3 0.2 - - - -
306A LYS* 1.4 74.4 - - + +
308A THR* 1.4 58.0 + - - +
310A ALA* 3.7 6.7 + - - +
311A TRP* 3.1 26.5 + - - +
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Residues in contact with THR 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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174A PHE* 3.7 9.8 - - + -
175A GLY* 3.4 46.8 - - - +
176A PRO* 5.1 1.8 - - - -
178A ASP* 5.3 1.3 - - - +
180A PHE* 4.6 15.0 - - + -
188A LEU* 6.5 0.7 - - + -
189A PRO* 6.2 1.6 - - + -
192A ILE* 5.8 4.0 - - + -
219A TYR* 3.6 5.5 - - - -
304A ALA 2.7 18.9 + - - -
305A VAL* 3.1 10.9 + - - -
307A GLU* 1.4 74.4 - - - +
309A CYS* 1.4 60.3 + - - +
311A TRP* 3.2 9.0 + - - +
312A PHE* 3.0 27.4 + - - +
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Residues in contact with CYS 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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192A ILE* 4.7 9.4 - - - -
259A VAL* 4.3 11.4 - - - -
262A ALA* 3.9 21.8 - - + +
263A MET* 3.6 38.0 - - + +
305A VAL* 2.8 36.8 + - - +
306A LYS 3.7 4.0 - - - +
308A THR* 1.4 71.7 - - - +
310A ALA* 1.4 61.0 + - - +
312A PHE* 3.2 8.0 + - - +
313A THR* 2.9 29.7 + - - -
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Residues in contact with ALA 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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306A LYS* 2.9 21.0 + - + +
307A GLU* 3.8 7.6 - - - +
309A CYS* 1.4 74.7 - - - +
311A TRP* 1.4 56.0 + - - +
313A THR* 3.5 6.2 + - - -
314A ASP* 2.9 31.2 + - - +
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Residues in contact with TRP 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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176A PRO* 3.6 34.2 - - + +
177A HIS* 3.3 56.3 - + - -
180A PHE* 4.0 21.5 - + - -
307A GLU 3.1 15.2 + - - +
308A THR* 3.2 9.6 + - - +
310A ALA* 1.4 72.1 - - - +
312A PHE* 1.3 63.9 + + - +
314A ASP* 4.3 4.0 - - - -
315A ASN* 2.7 75.2 + - + +
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Residues in contact with PHE 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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180A PHE* 3.5 52.9 - + + -
192A ILE* 4.1 13.0 - - + -
193A HIS* 3.4 47.1 - + + -
196A HIS* 3.6 32.7 + + + -
263A MET* 4.9 4.7 - - + -
308A THR 3.0 13.4 + - - +
309A CYS* 3.2 10.3 + - - +
311A TRP* 1.3 83.8 - + - +
313A THR* 1.3 62.0 + - - +
315A ASN 3.6 15.4 - - - -
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Residues in contact with THR 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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196A HIS* 4.3 23.2 + - + +
263A MET* 3.4 19.9 - - + +
309A CYS 2.9 18.0 + - - -
310A ALA* 4.0 5.4 - - - -
312A PHE* 1.3 76.3 - - - +
314A ASP* 1.4 62.0 + - - +
315A ASN 5.1 0.2 - - - -
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Residues in contact with ASP 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 ALA 2.9 19.4 + - - +
311A TRP* 3.9 2.5 - - + +
313A THR* 1.4 78.7 - - - +
315A ASN* 1.4 71.9 + - - +
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Residues in contact with ASN 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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177A HIS* 5.5 0.2 + - - -
311A TRP* 2.7 70.2 + - + +
312A PHE* 3.6 18.6 - - - -
313A THR 5.0 0.2 - - - -
314A ASP* 1.4 84.5 - - - +
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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