Contacts of the helix formed by residues 255 - 265 (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 PRO 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ARG* 5.1 0.4 - - - +
184A PHE* 3.9 8.4 - - + -
192A ALA* 4.3 23.1 - - + -
193A VAL* 3.9 21.3 - - + -
253A GLY 3.7 9.0 - - - +
254A ASN* 1.3 86.7 - - - +
256A ILE* 1.3 57.7 + - + +
258A VAL* 3.5 0.6 - - + +
259A SER* 2.8 37.6 + - - -
330A ILE* 4.1 16.5 - - + +
380A MET* 3.8 34.7 - - + +
381A THR* 5.2 2.2 - - + +
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Residues in contact with ILE 256 (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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254A ASN* 3.1 13.6 + - - +
255A PRO* 1.3 78.5 - - + +
257A LYS* 1.3 65.8 + - - +
259A SER* 3.0 5.0 + - - -
260A ARG* 2.8 27.8 + - + +
380A MET* 3.6 22.9 - - - -
381A THR 4.1 2.2 - - - +
382A ARG* 3.7 11.7 - - - +
383A PRO* 4.0 19.5 - - + -
384A ASP* 3.5 30.1 - - + +
411A PRO* 4.2 9.6 - - + +
426A PHE* 4.0 27.1 - - + -
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Residues in contact with LYS 257 (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* 4.8 15.7 - - - -
248A ASP* 4.7 17.0 + - - +
251A GLY* 4.0 22.3 - - - +
254A ASN* 3.3 26.4 + - + +
256A ILE* 1.3 80.3 - - - +
258A VAL* 1.3 57.3 + - - +
260A ARG* 4.0 5.6 - - + -
261A VAL* 2.8 53.1 + - + +
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Residues in contact with VAL 258 (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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184A PHE* 4.1 5.4 - - + -
242A MET* 4.6 7.2 - - + -
247A MET* 4.6 10.3 - - - +
251A GLY 4.3 0.7 - - - +
252A ARG* 3.4 36.8 - - + +
254A ASN 2.7 33.7 + - - +
255A PRO* 3.5 5.4 - - + +
257A LYS* 1.3 73.2 - - - +
259A SER* 1.3 54.0 + - - +
261A VAL* 4.1 0.5 - - - +
262A GLY* 2.6 34.7 + - - -
324A PHE* 4.1 12.4 - - + -
325A LEU* 5.3 0.4 - - + -
328A LEU* 3.9 27.4 - - + -
330A ILE* 4.1 12.6 - - + -
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Residues in contact with SER 259 (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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255A PRO 2.8 16.4 + - - -
256A ILE* 3.0 9.2 + - - -
258A VAL* 1.3 76.6 - - - +
260A ARG* 1.3 54.8 + - - +
263A SER* 2.4 40.2 + - - -
321A PHE* 3.8 20.6 - - - -
325A LEU* 4.5 10.3 - - - -
330A ILE* 5.2 0.9 - - - +
378A ALA* 5.2 1.8 - - - -
380A MET* 4.4 10.7 - - - +
395A VAL* 4.4 11.1 - - - +
411A PRO* 3.7 19.3 - - - +
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Residues in contact with ARG 260 (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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256A ILE* 2.8 19.0 + - + +
257A LYS* 3.4 7.6 - - + +
259A SER* 1.3 83.5 + - - +
261A VAL* 1.3 61.5 + - + +
263A SER* 3.1 10.9 + - - -
264A ALA 3.9 1.6 + - - -
404A ASP* 3.5 17.0 + - - -
408A ARG* 2.9 59.2 + - - +
410A GLY 2.8 34.3 + - - -
411A PRO* 3.8 10.5 - - + -
426A PHE* 3.5 36.5 - - + -
427A ASP* 3.1 24.2 + - - -
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Residues in contact with VAL 261 (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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245A ALA* 3.9 22.4 - - + -
247A MET* 3.3 38.6 - - + -
257A LYS* 2.8 40.9 + - + +
260A ARG* 1.3 76.4 - - + +
262A GLY* 1.3 69.1 + - - +
263A SER 3.3 0.4 - - - -
264A ALA* 3.6 10.6 + - - +
265A MET* 3.6 12.8 + - + +
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Residues in contact with GLY 262 (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 VAL* 4.9 4.2 - - - +
247A MET* 5.6 1.6 - - - -
258A VAL 2.6 24.3 + - - -
259A SER 3.9 0.4 - - - -
261A VAL* 1.3 74.7 - - - +
263A SER* 1.3 55.8 + - - +
265A MET* 2.9 28.4 + - - +
266A VAL* 3.8 6.1 + - - +
321A PHE* 3.8 7.9 - - - -
324A PHE* 4.0 24.2 - - - -
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Residues in contact with SER 263 (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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259A SER 2.4 27.7 + - - -
260A ARG* 3.1 5.4 + - - -
262A GLY* 1.3 73.4 - - - +
264A ALA* 1.3 57.4 + - - +
265A MET 3.3 1.2 + - - -
266A VAL* 3.3 11.2 + - - +
267A ASN 4.4 1.7 + - - -
321A PHE* 3.5 15.2 - - - -
395A VAL* 3.4 20.6 - - - +
397A SER* 3.4 21.9 - - - +
408A ARG* 3.0 38.7 - - - +
410A GLY 4.7 0.5 + - - -
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Residues in contact with ALA 264 (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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260A ARG 4.0 4.0 - - - +
261A VAL* 3.6 7.1 + - - +
262A GLY 3.2 0.8 + - - -
263A SER* 1.3 79.3 + - - +
265A MET* 1.3 63.9 + - + +
266A VAL 3.4 0.2 - - - -
267A ASN 3.9 13.8 - - - +
269A LYS* 6.1 0.2 - - - +
272A GLU 5.6 0.7 - - - +
273A GLY* 5.6 0.2 - - - -
407A TYR* 5.6 8.5 - - + -
408A ARG* 3.7 34.5 - - - +
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Residues in contact with MET 265 (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 VAL* 3.8 24.7 - - + +
244A ARG* 4.2 24.9 - - + -
245A ALA* 3.5 30.3 - - + +
261A VAL* 3.6 15.3 - - + +
262A GLY 2.9 9.5 + - - +
264A ALA* 1.3 79.7 - - + +
266A VAL* 1.3 63.8 + - - +
267A ASN 3.4 0.7 - - - -
272A GLU* 4.4 13.7 - - + +
273A GLY* 3.2 30.0 - - - +
274A VAL* 2.7 31.7 + - + +
302A TYR* 4.3 6.5 - - + +
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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