Contacts of the helix formed by residues 295 - 309 (chain A) in PDB entry 1GIA
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 THR 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ILE* 4.3 4.5 - - - -
293A SER* 3.0 28.1 + - - +
294A ASN* 1.3 82.5 - - - +
296A TYR* 1.3 65.0 + - - +
297A GLU* 4.2 8.2 + - - +
298A GLU* 3.5 24.1 + - - +
299A ALA* 3.0 24.6 + - - +
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Residues in contact with TYR 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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227A LEU* 5.2 0.2 - - + -
271A LYS* 3.4 47.2 - - + +
274A PHE* 3.5 33.8 - + - -
275A GLU* 4.0 34.8 - - + +
278A ILE* 4.1 13.4 - - + +
295A THR* 1.3 73.2 - - - +
297A GLU* 1.3 85.0 + - + +
300A ALA* 2.8 45.9 + - + +
323A PHE* 4.2 13.6 - + - +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 3.5 7.2 + - - +
296A TYR* 1.3 100.1 + - + +
298A GLU* 1.3 64.2 + - + +
300A ALA* 4.3 2.6 - - - +
301A ALA* 3.3 23.9 + - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A TYR* 3.5 13.8 + - + +
292A GLY* 3.7 8.1 - - - -
293A SER* 2.7 40.3 + - - +
295A THR* 3.5 15.7 + - - +
296A TYR 3.3 0.2 - - - -
297A GLU* 1.3 77.4 - - + +
299A ALA* 1.3 65.6 + - - +
301A ALA* 3.5 5.4 + - - +
302A TYR* 3.2 22.3 + - - +
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Residues in contact with ALA 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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274A PHE* 3.5 22.7 - - + -
278A ILE* 3.7 20.4 - - + -
283A LEU* 4.0 9.5 - - + +
290A TYR* 3.3 16.9 + - + +
293A SER 4.8 0.4 - - - +
295A THR 3.0 19.0 + - - +
298A GLU* 1.3 76.0 - - - +
300A ALA* 1.3 62.2 + - - +
302A TYR* 3.4 3.2 + - - +
303A ILE* 3.2 28.2 + - - +
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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
----------------------------------------------------------
227A LEU* 5.3 1.3 - - + -
274A PHE* 3.8 17.8 - - + -
296A TYR* 2.8 36.3 + - + +
297A GLU* 4.3 2.9 - - - +
299A ALA* 1.3 73.6 - - - +
301A ALA* 1.3 61.8 + - - +
303A ILE* 3.3 5.9 + - - +
304A GLN* 3.0 22.2 + - - +
323A PHE* 3.6 31.2 - - + -
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU 3.3 18.1 + - - +
298A GLU* 3.9 4.7 - - - +
299A ALA 3.4 0.2 - - - -
300A ALA* 1.3 78.7 - - - +
302A TYR* 1.3 60.9 + - - +
304A GLN* 3.4 15.1 + - - +
305A CYS* 3.1 31.5 + - - -
323A PHE* 4.8 1.1 - - - -
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Residues in contact with TYR 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.2 10.1 - - + -
287A TYR* 3.7 34.1 - + + +
289A GLU* 2.9 29.9 + - - +
290A TYR* 3.6 47.4 + + + -
291A ALA 5.5 0.7 - - - -
298A GLU 3.2 14.3 + - - +
299A ALA* 3.6 8.5 - - - +
300A ALA 3.3 0.2 - - - -
301A ALA* 1.3 73.9 - - - +
303A ILE* 1.3 61.0 + - - +
305A CYS* 3.3 8.1 + - + +
306A GLN* 3.0 55.9 + - + +
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Residues in contact with ILE 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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225A VAL* 5.7 0.2 - - + -
227A LEU* 3.9 23.8 - - + +
243A MET* 4.3 18.6 - - + -
268A LEU* 4.9 4.5 - - + -
274A PHE* 3.7 31.4 - - + -
283A LEU* 4.0 18.8 - - + -
287A TYR* 4.0 18.6 - - + +
299A ALA 3.2 12.2 + - - +
300A ALA 3.8 6.5 - - - +
302A TYR* 1.3 72.5 - - - +
304A GLN* 1.3 66.7 + - - +
306A GLN* 3.1 17.8 + - - +
307A PHE* 3.1 35.3 + - + -
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Residues in contact with GLN 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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266A LEU* 5.2 0.4 - - - +
268A LEU* 3.8 18.3 - - + +
300A ALA 3.0 12.7 + - - +
301A ALA* 3.5 16.6 - - - +
303A ILE* 1.3 77.1 - - - +
305A CYS* 1.3 61.1 + - - +
307A PHE* 3.2 3.6 + - - +
308A GLU* 2.8 60.6 + - + +
321A THR* 4.0 17.4 + - + -
323A PHE* 3.6 22.2 - - + -
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Residues in contact with CYS 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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301A ALA* 3.1 20.7 + - - +
302A TYR* 3.7 10.3 - - + +
303A ILE 3.2 0.2 - - - -
304A GLN* 1.3 80.5 - - - +
306A GLN* 1.3 62.3 + - - +
308A GLU* 4.4 8.3 - - - +
309A ASP* 2.9 34.0 + - - +
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Residues in contact with GLN 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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247A MET* 4.7 9.9 - - - +
287A TYR* 3.7 40.8 - - + +
289A GLU* 4.8 3.9 + - - +
302A TYR* 3.0 58.8 + - + +
303A ILE* 3.1 7.6 + - - +
305A CYS* 1.3 78.4 - - - +
307A PHE* 1.3 62.6 + - + +
309A ASP* 3.9 9.7 + - - +
310A LEU* 3.7 17.0 - - - +
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Residues in contact with PHE 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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225A VAL* 3.7 39.5 - - + -
243A MET* 3.9 20.4 - - - -
246A SER* 3.9 16.4 - - - -
247A MET* 3.7 35.0 - - + -
250A PHE* 3.5 35.4 - + + -
266A LEU* 3.8 21.1 - - + -
268A LEU* 4.6 4.7 - - + -
287A TYR* 4.2 3.6 - - - -
303A ILE* 3.1 27.5 + - + +
304A GLN* 3.8 6.3 - - - +
306A GLN* 1.3 75.8 - - - +
308A GLU* 1.3 66.1 + - - +
309A ASP 3.1 1.6 - - - -
310A LEU* 3.1 26.3 + - + +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.7 3.8 - - + -
304A GLN* 2.8 49.0 + - + +
305A CYS* 4.2 8.3 - - - +
307A PHE* 1.3 71.2 - - - +
309A ASP* 1.3 61.3 + - - +
310A LEU 3.2 1.0 + - - -
311A ASN* 3.3 19.9 + - - +
314A LYS* 3.6 12.6 - - - -
319A ILE* 4.5 28.7 - - + +
321A THR* 2.6 29.8 + - - +
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Residues in contact with ASP 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 CYS 2.9 18.5 + - - +
306A GLN* 3.9 8.7 - - - +
307A PHE 3.1 0.4 - - - -
308A GLU* 1.3 77.0 - - - +
310A LEU* 1.3 62.4 + - - +
311A ASN 3.2 7.6 + - - +
312A LYS* 5.9 0.3 - - - +
314A LYS* 3.2 26.1 + - - +
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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