Contacts of the helix formed by residues 255 - 265 (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 PRO 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B PHE* 3.5 25.4 - - + -
192B ALA* 4.1 25.1 - - + -
193B VAL* 4.1 16.6 - - + -
253B GLY 3.8 6.5 - - - +
254B ASN* 1.3 89.8 - - - +
256B ILE* 1.3 66.7 + - + +
258B VAL* 3.3 2.3 + - + +
259B SER* 3.0 27.9 + - - -
330B ILE* 4.6 5.2 - - + +
380B MET* 3.7 32.4 - - + +
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Residues in contact with ILE 256 (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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192B ALA* 6.5 0.2 - - + -
254B ASN* 3.1 18.5 + - - +
255B PRO* 1.3 77.0 - - + +
257B LYS* 1.3 60.1 + - + +
259B SER* 3.2 5.6 + - - -
260B ARG* 2.8 32.8 + - + +
380B MET* 3.6 16.2 - - + -
381B THR 3.4 25.4 - - - +
382B ARG* 4.0 21.1 - - - +
383B PRO* 4.6 8.5 - - + -
384B ASP* 4.6 9.6 - - - +
411B PRO* 4.2 4.6 - - + +
426B PHE* 3.6 33.0 - - + -
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Residues in contact with LYS 257 (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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247B MET* 3.3 26.2 - - + +
248B ASP* 4.9 16.9 + - - +
251B GLY* 4.3 13.8 - - - +
254B ASN* 3.4 23.3 + - + +
255B PRO 3.2 0.4 - - - -
256B ILE* 1.3 79.1 - - + +
258B VAL* 1.3 62.4 + - - +
259B SER 3.3 0.2 - - - -
260B ARG* 4.0 5.2 - - + -
261B VAL* 2.7 45.9 + - + +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.9 15.3 - - + -
242B MET* 4.5 6.9 - - - +
247B MET* 3.9 10.0 - - + +
251B GLY 4.4 0.2 - - - +
252B ARG* 4.0 24.0 - - + +
254B ASN 2.9 27.4 + - - +
255B PRO 3.8 3.6 - - - +
257B LYS* 1.3 75.7 - - - +
259B SER* 1.3 55.4 + - - +
261B VAL* 4.1 0.5 - - - +
262B GLY* 2.6 35.0 + - - -
324B PHE* 3.7 24.7 - - + -
328B LEU* 3.7 18.2 - - + -
330B ILE* 4.1 13.0 - - + -
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PRO 3.0 15.5 + - - -
256B ILE* 3.2 4.9 + - - -
258B VAL* 1.3 80.9 - - - +
260B ARG* 1.3 65.5 + - - +
263B SER* 2.9 32.9 + - - -
321B PHE* 4.1 19.1 - - - -
325B LEU* 4.3 12.6 - - - -
330B ILE* 5.1 1.1 - - - -
378B ALA* 5.2 1.8 - - - -
380B MET* 4.1 11.6 - - - +
395B VAL* 4.5 7.5 - - - +
411B PRO* 3.4 19.9 - - - +
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Residues in contact with ARG 260 (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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256B ILE* 2.8 28.2 + - + +
257B LYS* 4.0 5.8 - - + +
259B SER* 1.3 73.9 + - - +
261B VAL* 1.3 62.5 + - + +
263B SER* 3.1 16.4 + - - -
264B ALA* 3.8 2.1 + - - +
404B ASP* 3.7 19.0 + - - -
408B ARG* 2.9 58.0 + - - +
410B GLY 2.8 36.0 + - - -
411B PRO* 3.8 6.7 - - + -
426B PHE* 3.4 44.2 - - + -
427B ASP* 3.1 17.8 + - - -
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Residues in contact with VAL 261 (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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242B MET* 5.6 3.1 - - + -
245B ALA* 3.8 28.9 - - + +
247B MET* 4.1 25.8 - - + -
257B LYS* 2.7 43.1 + - + +
258B VAL 4.1 0.9 - - - +
260B ARG* 1.3 76.2 - - + +
262B GLY* 1.3 66.0 + - - +
264B ALA* 3.1 14.9 + - - +
265B MET* 3.5 10.9 + - + +
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Residues in contact with GLY 262 (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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241B VAL* 5.2 3.3 - - - +
242B MET* 6.0 1.1 - - - +
258B VAL 2.6 23.3 + - - -
261B VAL* 1.3 75.0 - - - +
263B SER* 1.3 64.1 + - - +
265B MET* 2.7 22.1 + - - +
266B VAL* 3.4 10.4 + - - +
321B PHE* 3.6 11.4 - - - -
324B PHE* 4.1 18.8 - - - -
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Residues in contact with SER 263 (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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259B SER 2.9 23.9 + - - -
260B ARG* 3.1 4.5 + - - -
262B GLY* 1.3 73.5 - - - +
264B ALA* 1.3 58.8 + - - +
265B MET 3.4 0.3 + - - -
266B VAL* 3.5 14.8 + - - +
267B ASN* 4.6 1.6 + - - +
321B PHE* 3.1 19.5 - - - -
395B VAL* 3.4 25.9 - - - +
397B SER* 3.9 14.9 - - - +
408B ARG* 2.9 37.9 - - - +
410B GLY 4.9 0.2 + - - -
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Residues in contact with ALA 264 (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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260B ARG 4.2 2.2 - - - +
261B VAL* 3.1 11.5 + - - +
262B GLY 2.8 2.0 + - - -
263B SER* 1.3 79.2 + - - +
265B MET* 1.3 61.9 + - + +
266B VAL 3.3 0.4 - - - -
267B ASN 3.9 7.2 - - - +
272B GLU* 3.2 21.6 - - - +
407B TYR* 5.4 9.2 - - + -
408B ARG* 3.9 30.3 - - + +
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Residues in contact with MET 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.9 35.0 - - + +
244B ARG* 4.0 14.1 - - + +
245B ALA* 3.8 28.5 - - + -
261B VAL* 3.8 13.0 - - + +
262B GLY 2.7 13.0 + - - +
264B ALA* 1.3 74.5 - - + +
266B VAL* 1.3 54.6 + - + +
267B ASN 3.3 1.6 - - - -
272B GLU* 4.0 27.4 - - + +
273B GLY* 2.7 19.8 - - - -
274B VAL* 2.6 37.3 + - + +
302B TYR* 3.8 23.1 - - + +
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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