Contacts of the helix formed by residues 293 - 308 (chain A) in PDB entry 3G9W
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 SER 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A PHE* 4.9 5.5 - - - +
246A GLN* 5.4 0.9 - - - -
291A GLU 3.5 2.9 + - - -
292A MET* 1.3 77.3 - - - +
294A GLU* 1.3 65.6 + - - +
295A ILE* 3.3 9.5 + - - +
296A GLU* 3.0 26.7 + - - +
297A ALA* 3.0 23.3 + - - +
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Residues in contact with GLU 294 (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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246A GLN 5.3 2.5 - - - +
247A ILE* 4.0 31.0 - - + +
293A SER* 1.3 74.1 - - - +
295A ILE* 1.3 61.7 + - + +
297A ALA* 3.4 6.7 + - - +
298A LYS* 3.0 63.1 + - + +
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Residues in contact with ILE 295 (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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198A LYS* 5.8 8.1 - - + -
199A PHE* 4.8 5.4 - - + +
208A SER* 4.2 28.7 - - - +
211A PRO* 4.5 26.7 - - + -
214A LEU* 3.6 24.6 - - + +
293A SER* 3.2 8.3 + - - +
294A GLU* 1.3 81.3 - - + +
296A GLU* 1.3 62.0 + - - +
298A LYS* 3.3 5.2 + - + +
299A VAL* 2.9 28.1 + - + +
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.4 54.4 - - + +
292A MET* 3.5 30.1 - - + +
293A SER* 3.0 22.8 + - - +
295A ILE* 1.3 76.9 - - - +
297A ALA* 1.3 63.5 + - - +
299A VAL* 3.3 2.8 + - - +
300A LYS* 3.0 51.8 + - - +
309B ARG* 3.9 17.7 + - - +
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Residues in contact with ALA 297 (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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243A PHE* 4.1 13.9 - - + +
246A GLN* 4.1 15.3 - - + -
247A ILE* 3.5 25.1 - - + -
292A MET* 3.6 20.3 - - - -
293A SER 3.0 16.5 + - - +
294A GLU* 3.7 1.3 - - - +
296A GLU* 1.3 77.4 - - - +
298A LYS* 1.3 57.3 + - - +
300A LYS* 3.3 2.3 + - - +
301A TYR* 2.9 30.0 + - - +
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Residues in contact with LYS 298 (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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214A LEU* 3.9 21.8 - - + -
215A ASN* 2.8 38.2 + - - +
218A TYR* 3.8 28.4 - - + -
247A ILE* 3.6 26.9 - - + -
294A GLU* 3.0 51.5 + - + +
295A ILE* 3.7 7.1 - - + +
296A GLU 3.3 0.2 - - - -
297A ALA* 1.3 71.3 - - - +
299A VAL* 1.3 66.9 + - - +
301A TYR* 3.3 3.3 + - - +
302A VAL* 3.0 28.8 + - - +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 3.9 17.9 - - + -
201A TYR* 3.8 28.3 - - + -
206A VAL* 4.6 8.5 - - + +
208A SER* 4.0 29.2 - - - +
214A LEU* 3.7 25.6 - - + -
295A ILE 2.9 17.4 + - - +
296A GLU 3.6 6.5 - - - +
298A LYS* 1.3 77.6 - - - +
300A LYS* 1.3 58.7 + - - +
302A VAL* 3.3 2.3 + - - +
303A LYS* 2.9 36.7 + - + +
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Residues in contact with LYS 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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199A PHE* 4.2 12.1 - - + -
243A PHE* 3.7 27.2 - - + -
292A MET* 3.9 23.6 - - + +
296A GLU* 3.0 46.5 + - + +
297A ALA 3.9 2.7 - - - +
299A VAL* 1.3 81.1 - - + +
301A TYR* 1.3 60.3 + - - +
303A LYS* 3.7 20.2 - - + +
304A LEU* 3.0 29.5 + - - +
307B SER* 3.6 22.2 + - - +
309B ARG* 4.6 7.9 - - - +
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Residues in contact with TYR 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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218A TYR* 3.7 27.8 - + + -
221A ALA* 4.1 6.5 - - + -
222A ARG* 3.2 49.5 + - + +
225A ILE* 3.7 20.5 - - + +
226A LEU* 5.0 2.1 - - - +
240A PHE* 3.4 56.8 - + + +
243A PHE* 3.7 19.7 - - + -
244A GLN* 4.4 11.2 + - + -
297A ALA 2.9 17.2 + - - +
298A LYS 3.6 5.2 - - - +
299A VAL 3.3 0.2 - - - -
300A LYS* 1.3 76.3 - - - +
302A VAL* 1.3 66.5 - - - +
304A LEU* 3.2 5.6 + - - +
305A ALA* 3.0 18.6 + - + +
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Residues in contact with VAL 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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205A ASN 5.4 0.4 - - - +
206A VAL* 4.0 26.5 - - + -
214A LEU* 4.4 5.6 - - + -
217A LEU* 3.9 19.3 - - + +
218A TYR* 3.8 34.1 - - + +
221A ALA* 4.8 6.5 - - + -
298A LYS 3.0 17.5 + - - +
299A VAL 3.7 3.4 - - - +
301A TYR* 1.3 76.1 - - - +
303A LYS* 1.3 61.0 + - - +
305A ALA* 3.4 6.8 + - - +
306A ARG* 2.9 47.3 + - + +
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Residues in contact with LYS 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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199A PHE* 6.1 0.8 - - + -
201A TYR* 3.5 59.2 - - + +
203A ASP* 4.9 2.2 - - - +
206A VAL* 4.2 9.0 - - + -
299A VAL* 2.9 28.0 + - + +
300A LYS* 3.7 21.7 - - + +
302A VAL* 1.3 73.8 - - - +
304A LEU* 1.3 66.0 + - - +
306A ARG* 3.5 6.8 + - - +
307A SER* 3.0 23.4 + - - -
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Residues in contact with LEU 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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236A LYS* 4.2 18.2 - - + -
239A GLU* 3.7 38.8 - - + +
240A PHE* 3.5 33.2 - - + +
243A PHE* 4.3 14.8 - - + -
300A LYS 3.0 17.9 + - - +
301A TYR* 3.6 4.7 - - - +
303A LYS* 1.3 76.6 - - - +
305A ALA* 1.3 64.2 + - - +
307A SER* 2.7 29.4 + - - +
308A LEU* 3.6 8.0 + - - +
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Residues in contact with ALA 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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221A ALA* 4.2 23.6 - - + -
225A ILE* 4.4 7.9 - - + -
230A HIS* 3.6 13.3 - - + +
240A PHE* 3.6 18.3 - - + -
301A TYR* 3.0 13.0 + - + +
302A VAL* 3.6 8.3 - - + +
304A LEU* 1.3 77.8 - - - +
306A ARG* 1.3 61.9 + - + +
307A SER 3.2 0.9 + - - -
308A LEU* 3.3 7.8 + - - +
311A TYR* 3.3 26.5 - - + +
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Residues in contact with ARG 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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205A ASN* 3.3 57.5 + - - +
206A VAL* 6.3 0.4 - - + -
217A LEU* 6.3 1.2 - - - +
302A VAL* 2.9 29.3 + - + +
303A LYS* 3.9 6.1 - - - +
305A ALA* 1.3 75.2 - - + +
307A SER* 1.3 61.4 + - - +
308A LEU 3.4 6.9 + - - +
311A TYR* 3.5 56.5 + - + +
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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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236A LYS* 5.8 0.2 - - - -
303A LYS 3.0 15.1 + - - -
304A LEU* 2.7 29.9 + - - +
306A ARG* 1.3 77.3 - - - +
308A LEU* 1.3 66.4 + - - +
309A ARG* 3.9 1.7 + - - +
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Residues in contact with LEU 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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230A HIS* 3.9 12.8 - - + +
232A VAL* 3.9 30.3 - - + -
236A LYS* 4.2 30.5 - - + -
240A PHE* 4.1 20.4 - - + -
304A LEU 3.7 8.5 - - - +
305A ALA 3.8 4.0 - - - +
306A ARG 3.2 3.9 - - - +
307A SER* 1.3 84.3 - - - +
309A ARG* 1.3 65.5 + - - +
310A THR* 3.5 15.0 - - - +
311A TYR* 3.1 18.9 + - - +
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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