Contacts of the helix formed by residues 295 - 304 (chain A) in PDB entry 1GGT
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A TRP* 3.0 20.5 + - - -
226A SER 2.8 8.2 + - - -
227A TYR 3.9 3.6 - - - -
294A GLY* 1.3 70.1 - - - -
296A VAL* 1.3 64.8 + - - +
297A ASP 3.2 2.7 - - - -
298A ILE* 3.0 5.5 + - - +
299A LEU* 3.0 26.7 + - - +
319A GLY 3.2 11.1 + - - -
320A VAL* 3.4 17.8 + - - -
323A THR* 2.8 32.8 + - - -
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A SER* 4.3 9.4 - - - +
227A TYR 4.3 0.7 - - - +
228A GLY* 3.5 40.2 - - - +
231A GLU* 4.0 8.7 - - + -
234A ILE* 4.0 16.6 - - + -
294A GLY 3.7 1.2 - - - -
295A SER* 1.3 76.1 - - - +
297A ASP* 1.3 58.8 + - - +
299A LEU* 4.0 0.6 - - - -
300A LEU* 2.9 58.7 + - + +
323A THR* 5.8 0.2 - - - +
668A ASP* 5.5 3.1 - - - +
670A PRO* 5.7 0.4 - - + -
674A ARG* 4.3 18.6 - - - +
675A PRO* 4.5 16.4 - - + -
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Residues in contact with ASP 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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292A TRP* 3.6 23.9 - - + -
293A THR* 4.8 7.0 + - - +
294A GLY 4.5 6.7 + - - +
296A VAL* 1.3 79.7 - - - +
298A ILE* 1.3 59.1 + - - +
300A LEU* 4.0 3.8 - - - +
301A GLU* 3.1 33.7 + - - +
666A HIS* 5.0 2.6 + - - -
668A ASP* 5.4 1.3 + - - +
675A PRO* 4.0 29.4 - - + +
677A LYS* 2.6 41.4 + - - +
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Residues in contact with ILE 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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225A TRP* 4.3 1.6 - - + -
274A VAL* 4.0 14.6 - - + -
275A LEU* 3.9 29.2 - - + -
292A TRP* 3.7 49.1 - - + +
294A GLY 3.7 16.8 - - - +
295A SER 3.0 5.5 + - - +
297A ASP* 1.3 74.3 - - - +
299A LEU* 1.3 55.0 + - - +
301A GLU* 3.1 4.8 + - - -
302A TYR* 2.8 31.0 + - - +
309A VAL* 3.4 14.0 - - + +
316A VAL* 3.9 15.3 - - + -
320A VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 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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234A ILE* 3.8 31.2 - - + -
237A THR* 3.4 32.5 - - + +
238A CYS* 4.9 9.6 - - - -
241A VAL* 4.9 8.1 - - + -
274A VAL* 4.4 16.4 - - + -
295A SER* 3.0 20.9 + - - +
296A VAL 4.1 1.8 - - - +
298A ILE* 1.3 75.3 - - - +
300A LEU* 1.3 63.9 + - - +
302A TYR* 3.3 6.0 + - + +
303A ARG* 3.1 18.5 + - - +
320A VAL* 4.0 27.6 - - + +
323A THR* 3.9 19.7 - - + -
324A PHE* 5.2 4.5 - - + +
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Residues in contact with LEU 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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232A ASP* 4.3 6.1 - - - +
233A GLY* 4.4 5.6 - - - +
234A ILE* 3.9 17.7 - - + -
237A THR* 3.9 15.3 - - - +
296A VAL* 2.9 39.4 + - + +
297A ASP* 4.1 3.8 - - - +
299A LEU* 1.3 73.1 - - - +
301A GLU* 1.3 58.9 + - - +
302A TYR 3.2 0.5 + - - -
303A ARG* 3.4 17.8 + - - +
304A SER* 2.6 33.8 + - - +
674A ARG* 4.0 23.3 - - - +
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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
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287A VAL* 5.0 6.9 - - - +
292A TRP* 4.2 15.8 - - + -
297A ASP* 3.1 21.8 + - - +
298A ILE* 3.4 9.4 - - - +
300A LEU* 1.3 74.2 - - - +
302A TYR* 1.3 55.1 + - - +
304A SER* 4.1 3.8 + - - -
305A SER* 2.5 42.7 + - - -
309A VAL* 3.6 21.7 - - + +
310A ARG 5.7 0.3 + - - -
677A LYS* 5.2 5.2 + - - +
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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
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237A THR* 4.5 7.6 - - + -
240A TYR* 3.6 26.5 - + - -
241A VAL* 4.1 16.9 - - + -
244A ARG* 3.2 34.1 + - - +
265A MET* 4.3 10.2 - - - +
271A ASP 5.9 0.7 - - - -
273A GLY 3.5 27.5 + - - -
274A VAL* 4.0 24.0 - - + -
298A ILE 2.8 12.8 + - - +
299A LEU* 3.5 14.1 - - + +
300A LEU 3.1 0.2 - - - -
301A GLU* 1.3 77.6 - - - +
303A ARG* 1.3 59.8 + - - +
305A SER* 3.9 3.1 - - - -
306A GLU* 2.7 32.8 + - - -
307A ASN* 3.7 24.2 - - - -
309A VAL* 3.6 9.8 - - + +
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Residues in contact with ARG 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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233A GLY* 3.6 23.0 + - - -
236A ASP* 3.3 30.5 + - - +
237A THR* 3.7 19.1 + - + +
240A TYR* 4.1 41.1 - - + -
299A LEU 3.1 15.5 + - - +
300A LEU* 3.4 13.6 + - - +
302A TYR* 1.3 75.0 - - - +
304A SER* 1.3 67.0 + - - +
306A GLU* 3.1 19.4 - - - +
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Residues in contact with SER 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 LEU* 2.6 20.2 + - - +
301A GLU* 4.2 3.3 - - - -
303A ARG* 1.3 80.8 + - - +
305A SER* 1.3 62.1 + - - +
306A GLU* 3.9 6.1 - - - +
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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