Contacts of the helix formed by residues 295 - 304 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B TRP* 3.3 8.3 + - - +
226B SER 2.8 9.5 + - - -
227B TYR 3.6 7.6 + - - -
294B GLY* 1.3 69.6 - - - -
296B VAL* 1.3 65.0 + - - +
297B ASP 3.3 2.5 - - - -
298B ILE* 3.0 17.8 + - - +
299B LEU* 3.0 18.8 + - - +
319B GLY 2.9 24.3 + - - -
320B VAL* 3.4 8.4 + - - -
323B THR* 2.6 36.2 + - - -
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B SER* 4.1 11.2 - - - +
227B TYR 4.4 1.3 - - - +
228B GLY* 3.9 34.8 - - - +
231B GLU* 4.0 19.7 - - + -
234B ILE* 4.2 14.6 - - + -
294B GLY* 3.6 0.8 - - - -
295B SER* 1.3 74.8 - - - +
297B ASP* 1.3 66.2 + - - +
299B LEU* 3.3 0.3 + - - -
300B LEU* 3.1 47.8 + - + +
668B ASP* 5.7 2.9 - - - +
670B PRO* 6.0 0.2 - - + -
674B ARG* 5.1 5.8 - - - +
675B PRO* 4.4 22.4 - - + -
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B TRP* 3.5 32.7 - - + -
293B THR* 4.6 6.7 + - - +
294B GLY 4.2 8.2 - - - +
296B VAL* 1.3 81.3 - - - +
298B ILE* 1.3 60.2 + - - +
300B LEU* 4.0 3.5 - - - +
301B GLU* 3.3 22.8 + - - +
666B HIS* 4.5 13.9 + - - -
668B ASP* 5.5 0.6 + - - +
675B PRO* 3.4 38.4 - - + +
677B LYS* 5.3 6.5 - - - +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B TRP* 4.4 2.9 - - + -
274B VAL* 4.4 8.3 - - + -
275B LEU* 3.7 28.0 - - + -
292B TRP* 3.9 32.3 - - + -
294B GLY 3.9 17.0 - - - +
295B SER 3.0 7.1 + - - +
297B ASP* 1.3 74.0 - - - +
299B LEU* 1.3 59.7 + - - +
301B GLU* 3.5 3.9 + - - -
302B TYR* 2.9 26.9 + - - +
309B VAL* 3.5 13.2 - - + +
316B VAL* 3.7 24.7 - - + -
320B VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ILE* 3.7 39.9 - - + -
237B THR* 3.8 20.4 + - - +
238B CYS* 4.8 7.0 - - - -
241B VAL* 5.2 12.1 - - + -
274B VAL* 4.4 13.5 - - + -
295B SER* 3.0 22.8 + - - +
298B ILE* 1.3 69.7 - - - +
300B LEU* 1.3 66.9 + - - +
302B TYR* 3.1 9.8 + - + +
303B ARG* 2.9 24.3 + - - +
320B VAL* 3.7 27.1 - - + +
323B THR* 3.7 21.1 - - + -
324B PHE* 5.4 2.5 - - + +
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B ASP 4.4 9.6 - - - +
233B GLY* 4.4 6.1 - - - +
234B ILE* 4.0 18.4 - - + -
237B THR* 4.3 14.4 - - + -
296B VAL* 3.1 36.1 + - + +
297B ASP* 4.0 3.8 - - - +
299B LEU* 1.3 76.0 - - - +
301B GLU* 1.3 57.3 + - - +
303B ARG* 3.3 4.9 + - + +
304B SER* 2.9 36.0 + - - +
674B ARG* 4.0 29.2 - - - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B TRP* 5.5 7.0 - - + -
297B ASP 3.3 16.7 + - - +
298B ILE* 3.5 6.7 - - - +
300B LEU* 1.3 77.0 - - - +
302B TYR* 1.3 64.8 + - - +
304B SER* 4.7 4.9 - - - -
305B SER* 2.8 42.6 + - - -
309B VAL* 3.7 25.7 - - + +
310B ARG 5.4 0.5 + - - -
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B THR* 5.4 2.5 - - - -
240B TYR* 3.4 30.5 - + - -
241B VAL* 4.0 21.1 - - + -
244B ARG* 3.5 36.4 + - - +
265B MET* 3.8 18.5 - - - +
272B GLU 4.2 1.0 + - - -
273B GLY 3.7 18.2 - - - -
274B VAL* 4.0 29.6 - - + -
298B ILE 2.9 14.7 + - - +
299B LEU* 3.2 15.5 - - + +
301B GLU* 1.3 76.1 - - - +
303B ARG* 1.3 55.9 + - + +
305B SER* 3.3 4.8 + - - -
306B GLU* 2.5 37.8 + - - -
307B ASN 3.4 23.1 - - - -
309B VAL* 3.9 4.9 - - + +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B GLY 4.7 0.4 + - - -
236B ASP* 4.0 18.0 + - - +
237B THR* 3.4 42.5 - - + +
240B TYR* 3.2 50.5 - - - +
299B LEU 2.9 15.6 + - - +
300B LEU* 3.7 8.3 - - + +
302B TYR* 1.3 73.5 - - - +
304B SER* 1.3 67.4 + - - +
306B GLU* 3.2 19.8 - - - +
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 2.9 19.2 + - - +
301B GLU* 3.9 7.0 - - - -
303B ARG* 1.3 81.1 - - - +
305B SER* 1.3 61.1 + - - +
306B GLU* 3.5 6.4 + - - +
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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