Contacts of the helix formed by residues 300 - 308 (chain A) in PDB entry 3GUU
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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247A ASP* 3.5 24.0 - - + +
248A MET* 3.6 15.5 - - - +
251A PHE* 3.7 26.9 - - + -
299A ALA* 1.4 84.3 - - + +
301A ILE* 1.3 63.2 + - + +
302A ALA 3.5 1.3 - - - -
303A SER* 3.0 23.5 + - - +
304A ILE* 3.1 14.4 + - + +
443A GOL 3.6 19.1 - - - +
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Residues in contact with ILE 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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248A MET* 4.3 23.3 - - + -
251A PHE* 4.2 18.4 - - + -
252A ILE* 4.3 15.5 - - + -
295A LEU* 3.6 44.6 - - + +
296A LEU* 4.2 10.1 - - + -
298A GLU 3.2 9.7 + - - +
300A PRO* 1.3 75.2 - - + +
302A ALA* 1.3 67.8 + - - +
304A ILE* 3.0 9.8 + - - +
305A LEU* 2.8 44.9 + - + +
442A 1PE 4.7 10.5 - - - +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU 3.5 19.5 - - - +
297A ASN* 3.8 13.5 - - - +
298A GLU 2.8 21.0 + - - +
299A ALA* 5.3 0.4 - - - -
301A ILE* 1.3 74.7 - - - +
303A SER* 1.3 61.6 + - - +
305A LEU* 3.3 8.7 + - - +
306A LYS* 3.3 33.5 + - - +
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Residues in contact with SER 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 ALA* 5.4 4.3 - - - +
300A PRO* 3.0 21.3 + - - +
302A ALA* 1.3 75.8 - - - +
304A ILE* 1.3 67.2 + - - +
306A LYS* 3.4 18.8 + - - +
307A GLN* 3.4 23.6 + - - +
316A SER* 4.5 0.7 + - - -
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Residues in contact with ILE 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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241A LEU* 4.9 6.3 - - + -
245A HIS* 3.7 40.4 - - + +
248A MET* 3.6 34.1 - - + -
300A PRO* 3.1 17.6 + - + +
301A ILE* 3.0 7.7 + - - +
303A SER* 1.3 81.7 + - - +
305A LEU* 1.3 63.2 + - + +
307A GLN* 3.0 12.0 + - - +
308A GLU* 2.8 36.1 + - + +
443A GOL 3.3 34.3 - - - +
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Residues in contact with LEU 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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218A ALA* 4.1 15.0 - - + -
219A LYS* 3.8 33.3 + - + +
241A LEU* 3.9 20.4 - - + -
248A MET* 6.0 0.9 - - + -
296A LEU* 4.4 13.9 - - + +
301A ILE* 2.8 45.0 + - + +
302A ALA* 3.3 11.4 + - - +
304A ILE* 1.3 76.3 - - + +
306A LYS* 1.3 59.7 + - + +
308A GLU* 3.4 14.7 + - + +
309A THR* 3.7 6.2 - - - +
314A GLU* 3.7 15.0 - - - +
442A 1PE 3.9 26.9 - - - -
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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
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302A ALA* 3.3 22.7 + - - +
303A SER* 3.6 12.6 - - - +
304A ILE 3.1 0.8 - - - -
305A LEU* 1.3 75.7 - - + +
307A GLN* 1.3 58.3 + - - +
309A THR* 3.5 5.5 - - - +
314A GLU* 3.7 22.7 - - + +
315A ALA* 3.3 10.7 - - - +
316A SER* 3.0 49.6 + - - +
317A TYR* 3.8 0.7 - - - -
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Residues in contact with GLN 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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153A TYR* 2.7 43.9 + - + +
192A TRP* 3.4 4.3 - - - -
245A HIS* 4.3 9.9 - - + -
303A SER* 3.4 14.1 - - - +
304A ILE* 3.0 23.2 + - - +
306A LYS* 1.3 75.7 - - - +
308A GLU* 1.3 58.1 + - + +
309A THR 3.0 10.9 + - - -
316A SER* 3.9 10.2 + - - +
317A TYR* 3.4 9.8 - - + -
443A GOL 4.9 1.7 + - - -
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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
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64A THR* 4.4 2.1 - - - +
150A ILE 3.8 3.0 - - - +
151A ALA* 4.0 8.1 - - - +
152A GLY* 3.0 28.0 + - - -
153A TYR* 3.9 18.0 - - + -
188A HIS* 5.2 3.1 + - - -
192A TRP* 3.9 10.0 + - - -
216A VAL 4.4 1.0 - - - +
218A ALA* 3.2 38.3 + - + +
241A LEU* 3.8 17.5 - - + +
245A HIS* 2.6 28.8 + - + +
304A ILE* 2.8 35.0 + - + +
305A LEU* 3.4 6.2 + - - +
307A GLN* 1.3 75.2 - - + +
309A THR* 1.3 57.0 + - - +
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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