Contacts of the helix formed by residues 295 - 306 (chain A) in PDB entry 3GIA
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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97A TYR* 3.5 32.3 - - - -
206A VAL* 4.8 1.6 - - - -
209A ASN* 4.7 1.3 - - - +
290A ALA 3.4 8.5 + - - -
291A THR 3.4 6.0 + - - -
294A GLY* 1.3 78.3 - - - +
296A ALA* 1.3 66.2 + - - +
297A ASN 3.3 0.9 - - - -
298A VAL* 3.3 5.5 + - - +
299A ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 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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94A TRP* 3.8 4.8 - - + -
97A TYR* 3.7 24.0 - - + -
101A ILE* 4.4 2.2 - - + -
291A THR 2.7 18.6 + - - +
292A ILE* 3.9 9.6 - - - +
295A GLY* 1.3 71.7 - - - +
297A ASN* 1.3 63.1 + - - +
299A ALA* 4.5 1.6 - - - -
300A TYR* 3.0 28.4 + - - +
317A TRP* 3.7 5.1 - - + -
327A THR* 3.9 28.3 - - + +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE 3.1 11.7 + - - -
293A TYR* 3.8 2.0 - - - +
294A GLY* 2.9 19.6 + - - +
295A GLY 3.5 3.6 + - - -
296A ALA* 1.3 74.5 - - - +
298A VAL* 1.3 69.2 + - - +
300A TYR* 4.1 1.6 - - - +
301A SER* 3.4 21.0 + - - -
314A ARG* 2.9 21.6 + - - +
316A VAL 2.7 29.8 + - - +
317A TRP* 3.6 39.0 + - + -
318A PHE* 3.7 20.8 - - + +
319A LYS 5.4 0.3 - - - +
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Residues in contact with VAL 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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69A ASN* 3.3 28.0 - - + +
209A ASN* 3.6 20.2 - - - +
294A GLY* 3.8 16.8 - - - +
295A GLY 3.3 6.7 + - - +
297A ASN* 1.3 92.2 + - - +
299A ALA* 1.3 63.5 + - - +
301A SER 3.3 2.1 + - - -
302A LEU* 3.1 20.5 + - + +
308A LEU* 3.4 21.2 - - + +
312A PHE* 3.8 28.9 - - + -
314A ARG* 5.4 2.7 - - + -
318A PHE* 3.9 7.2 - - + -
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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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90A SER 4.3 2.7 - - - +
93A LEU* 4.3 11.7 - - + -
94A TRP* 3.7 32.1 - - - +
97A TYR* 3.8 15.9 - - + -
209A ASN* 4.9 3.4 - - - +
295A GLY 3.0 17.5 + - - +
296A ALA 4.1 1.3 - - - +
298A VAL* 1.3 78.4 - - - +
300A TYR* 1.3 58.9 + - - +
302A LEU* 4.0 6.9 - - - +
303A ALA* 3.0 30.0 + - - +
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Residues in contact with TYR 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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94A TRP* 3.7 40.5 - + + +
296A ALA 3.0 18.3 + - - +
297A ASN 4.1 0.7 - - - +
299A ALA* 1.3 76.6 - - - +
301A SER* 1.3 60.8 + - - +
303A ALA* 3.3 3.5 + - - +
304A LYS* 2.8 43.9 + - + +
317A TRP* 3.8 17.7 - + + -
320A SER* 3.8 10.3 - - - -
322A GLU* 2.6 34.9 + - - +
323A GLY* 3.3 25.6 - - - -
326A ILE* 4.0 8.6 - - + +
800A D10 3.2 47.0 - - + +
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Residues in contact with SER 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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297A ASN 3.4 13.9 + - - -
298A VAL 3.3 1.2 + - - -
300A TYR* 1.3 82.7 - - - +
302A LEU* 1.3 58.4 + - - +
304A LYS* 4.5 3.6 - - - -
305A ASP* 2.8 43.1 + - - +
307A GLU 4.1 2.7 - - - -
308A LEU* 3.8 16.8 - - - -
309A PRO* 5.4 1.1 - - - -
318A PHE* 3.9 8.0 - - - -
319A LYS* 3.6 37.9 + - - +
320A SER* 4.6 3.5 + - - -
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Residues in contact with LEU 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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70A ALA* 3.6 39.3 - - + +
73A ILE* 3.7 31.4 - - + -
90A SER* 4.4 5.4 - - - -
93A LEU* 5.4 3.4 - - + -
209A ASN* 5.7 0.7 - - - +
298A VAL* 3.1 17.0 + - + +
299A ALA* 4.0 7.4 - - - +
301A SER* 1.3 74.5 - - - +
303A ALA* 1.3 60.5 + - - +
306A GLY* 2.8 31.1 + - - -
307A GLU* 3.8 28.7 - - - +
308A LEU* 3.8 12.7 - - + +
427A PHE* 3.5 6.9 - - + -
431A MET* 3.8 17.3 - - + -
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Residues in contact with ALA 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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90A SER* 3.4 35.9 - - - +
91A ILE* 4.0 15.4 - - + +
94A TRP* 4.8 2.5 - - + -
299A ALA 3.0 19.2 + - - +
300A TYR* 3.7 4.9 - - - +
302A LEU* 1.3 77.7 - - - +
304A LYS* 1.3 55.5 + - - +
419A TYR* 4.1 1.6 - - - -
425A ARG* 2.7 37.1 + - - -
800A D10 4.4 11.2 - - + +
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Residues in contact with LYS 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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300A TYR* 2.8 28.2 + - + +
301A SER* 3.9 3.8 - - - +
303A ALA* 1.3 77.9 - - - +
305A ASP* 1.3 69.7 + - - +
320A SER* 3.0 26.4 + - - +
322A GLU* 2.7 34.1 + - - +
419A TYR* 2.9 35.6 + - - +
425A ARG* 3.3 15.2 - - - +
800A D10 3.7 41.1 - - + +
803A D10 5.4 6.7 - - - -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 2.8 27.8 + - - +
304A LYS* 1.3 95.5 - - - +
306A GLY* 1.3 58.5 + - - +
307A GLU* 3.1 29.6 + - + +
309A PRO* 6.0 0.5 - - - +
319A LYS* 2.7 40.1 + - - +
320A SER* 4.8 2.0 + - - -
425A ARG* 3.6 10.9 - - - +
426A THR 4.2 2.9 - - - +
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Residues in contact with GLY 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 2.8 25.0 + - - +
305A ASP* 1.3 69.8 - - - +
307A GLU* 1.3 62.1 + - - +
425A ARG* 3.5 13.7 - - - +
426A THR 3.4 23.4 - - - +
427A PHE* 3.6 26.1 - - - -
428A SER 4.3 3.8 + - - -
431A MET* 4.4 4.3 - - - +
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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