Contacts of the helix formed by residues 295 - 307 (chain A) in PDB entry 2W8D
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 GLY 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A GLN* 1.3 72.3 - - - +
296A LYS* 1.3 66.9 + - - +
297A TPO 3.1 1.0 + - - -
298A SER* 2.9 24.5 + - - -
299A ASP* 2.8 30.0 + - - -
314A GLY 4.1 4.6 + - - -
315A SER* 4.0 13.5 - - - -
350A TRP* 3.6 17.3 - - - -
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Residues in contact with LYS 296 (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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292A THR* 3.5 13.6 + - - +
293A GLY 3.2 23.2 + - - +
294A GLN* 3.2 13.7 - - - +
295A GLY* 1.3 73.0 - - - +
297A TPO 1.3 80.7 + - - +
299A ASP* 3.2 5.3 + - - +
300A ALA* 3.2 17.7 + - - +
350A TRP* 4.4 3.8 - - + -
472A HIS* 3.7 32.4 - - + +
473A TYR* 2.7 44.3 + - - -
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Residues in contact with TPO 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A SER* 4.4 6.5 - - - +
253A GLU* 3.0 5.3 + - - +
295A GLY 3.1 0.4 + - - -
296A LYS* 1.3 82.9 - - - +
298A SER* 1.3 57.3 + - - -
300A ALA* 3.3 6.2 + - - +
301A GLU* 3.1 27.9 + - + +
349A PHE* 4.6 7.4 - - - -
350A TRP* 3.0 28.4 + - - -
352A ARG* 3.5 24.7 + - - +
407A ILE* 3.8 19.5 - - + -
409A LEU* 5.7 0.2 - - - +
412A HIS* 2.9 35.7 + - - -
469A TYR* 5.3 0.3 + - - -
471A ASP* 3.4 18.5 - - - +
472A HIS* 3.3 7.3 + - - -
1636A MG 2.0 51.9 - - - -
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Residues in contact with SER 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLY* 2.9 20.4 + - - -
297A TPO 1.3 78.2 + - - -
299A ASP* 1.3 59.1 + - - +
301A GLU* 3.3 12.0 + - - -
302A PHE* 2.8 24.8 + - - +
315A SER* 4.1 1.0 + - - -
317A PHE* 3.2 45.0 - - - +
350A TRP* 3.5 33.3 - - - +
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Residues in contact with ASP 299 (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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292A THR* 3.7 13.5 - - + -
293A GLY* 2.8 26.5 + - - -
294A GLN 3.5 0.5 + - - -
295A GLY* 2.8 37.9 + - - -
296A LYS 3.4 8.5 - - - +
298A SER* 1.3 74.5 + - - +
300A ALA* 1.3 62.1 + - - +
302A PHE* 3.3 6.2 + - - +
303A MSE 3.2 27.7 + - - +
310A PRO* 3.4 29.0 - - + +
311A LEU 4.9 1.4 - - - +
314A GLY 4.9 1.1 - - - +
315A SER* 4.6 0.5 - - - -
316A VAL* 3.8 14.8 + - - +
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Residues in contact with ALA 300 (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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292A THR* 3.5 8.2 - - + +
296A LYS 3.2 5.0 + - - +
297A TPO 3.3 7.2 + - - +
299A ASP* 1.3 77.6 - - - +
301A GLU* 1.3 64.9 + - - +
303A MSE 3.2 10.6 + - - +
304A MSE 3.1 27.7 + - + +
469A TYR* 4.0 20.2 - - + -
471A ASP* 3.6 28.5 - - + +
523A ASP* 4.3 9.6 - - - +
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A SER* 5.7 0.4 - - - -
297A TPO 3.1 19.8 + - + +
298A SER* 3.3 12.5 + - - +
300A ALA* 1.3 76.1 - - - +
302A PHE* 1.3 63.3 + - - +
304A MSE 3.3 5.0 + - - +
305A GLU* 3.1 28.6 + - + +
317A PHE* 4.0 12.1 - - + -
352A ARG* 2.8 35.8 + - - -
356A TYR* 2.5 30.7 + - + -
405A LYS* 2.8 26.5 + - - +
407A ILE* 3.7 13.9 - - + +
469A TYR* 4.1 14.8 + - - +
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Residues in contact with PHE 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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298A SER 2.8 17.3 + - - +
299A ASP 3.5 5.4 - - - +
300A ALA 3.2 0.4 - - - -
301A GLU* 1.3 76.5 - - - +
303A MSE 1.3 57.8 + - + +
306A ASN* 2.9 61.5 + - + +
308A LEU* 3.4 34.5 - - + -
309A TYR 3.7 17.5 - - - -
310A PRO 4.3 1.3 - - - -
316A VAL* 3.7 43.1 - - + -
317A PHE* 3.8 10.0 - + + -
320A LYS* 5.9 0.7 - - + -
325A LEU* 4.2 16.2 - - + -
355A MSE 4.0 18.2 - - + -
359A GLU* 3.9 7.0 - - - -
609A ILE* 4.0 16.2 - - + -
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Residues in contact with MSE 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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291A GLN* 3.6 32.8 - - - +
292A THR* 3.7 13.2 - - + +
299A ASP 3.2 21.6 + - - +
300A ALA* 3.7 4.9 - - - +
301A GLU 3.2 0.2 - - - -
302A PHE* 1.3 76.0 - - + +
304A MSE 1.3 61.3 + - - +
307A SER* 2.9 27.3 + - - +
308A LEU 3.2 23.8 - - - +
309A TYR* 4.4 0.9 - - - -
310A PRO* 3.6 20.4 - - + -
523A ASP* 3.4 50.9 - - + +
524A VAL* 3.7 21.7 - - + -
527A ALA* 4.5 2.6 - - - +
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Residues in contact with MSE 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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249A TYR* 3.8 28.2 + - + -
288A PHE* 4.6 0.2 - - + -
300A ALA 3.1 23.3 + - - +
301A GLU* 3.3 6.0 + - - +
303A MSE 1.3 76.3 - - - +
305A GLU* 1.3 73.4 + - - +
328A VAL* 4.0 2.9 - - - +
403A TYR* 4.4 0.2 + - - -
405A LYS* 5.8 0.2 - - - +
469A TYR* 3.7 47.3 - - + +
523A ASP* 3.2 48.7 - - + +
526A VAL* 3.7 28.5 - - + -
527A ALA* 3.3 27.9 - - - +
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Residues in contact with GLU 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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249A TYR* 5.3 1.0 - - - -
301A GLU* 3.1 15.5 + - + +
304A MSE 1.3 89.3 - - - +
306A ASN* 1.3 59.7 + - - +
326A GLN 4.8 0.2 - - - +
327A SER* 3.3 14.6 - - - -
328A VAL* 3.1 29.9 + - - +
329A PRO* 3.4 10.9 - - + +
359A GLU* 3.5 35.9 - - - +
361A ILE* 5.1 0.9 - - + -
403A TYR* 2.2 34.6 + - - -
405A LYS* 3.1 42.5 + - + +
543A MSE 5.1 0.2 - - - +
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Residues in contact with ASN 306 (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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302A PHE* 2.9 44.9 + - + +
303A MSE 3.4 0.2 + - - -
305A GLU* 1.3 81.6 - - - +
307A SER* 1.3 71.0 + - - +
308A LEU* 3.3 27.8 + - + +
325A LEU* 4.0 17.4 - - - +
326A GLN 4.5 3.6 + - - +
327A SER* 3.1 23.1 + - - +
359A GLU* 2.9 28.5 + - - -
527A ALA* 5.2 0.2 - - - -
542A LEU 4.6 0.9 - - - +
543A MSE 3.8 15.7 - - - +
614A LEU* 6.0 0.3 - - - +
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Residues in contact with SER 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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303A MSE 2.9 15.7 + - - -
305A GLU 4.0 0.6 - - - -
306A ASN* 1.3 78.9 - - - +
308A LEU* 1.3 59.9 + - - +
524A VAL* 2.7 32.5 + - - -
527A ALA* 4.4 3.5 - - - +
528A PRO* 3.9 7.6 - - - +
543A MSE 3.5 25.4 - - - +
544A SER* 2.6 35.4 + - - -
545A GLY* 2.8 22.2 + - - -
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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