Contacts of the helix formed by residues 316 - 329 (chain B) in PDB entry 1GGE
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 ASP 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 2.8 30.8 + - - +
177B ASP* 3.1 9.4 - - - -
314B ASP* 3.0 13.4 + - - +
315B PRO* 1.3 79.8 - - - +
317B PHE* 1.3 55.3 + - - -
319B ARG 3.2 1.9 + - - -
320B ARG* 2.8 28.5 + - - +
228C ALA 4.4 2.4 - - - +
229C ILE* 3.8 29.8 - - + +
230C PRO* 3.1 12.4 - - - +
231C GLN* 2.8 36.7 + - - +
233C GLN* 4.1 5.9 + - - -
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP* 3.4 1.8 + - - +
178B THR* 3.8 8.1 - - + -
264B ARG* 3.4 48.5 - - - -
302B LEU* 4.9 2.7 - - + -
310B LEU* 3.6 36.3 - - + -
314B ASP* 3.0 33.0 + - - +
315B PRO 3.4 1.0 - - - -
316B ASP* 1.3 76.8 - - - +
318B HIS* 1.3 70.3 + + - +
320B ARG* 3.5 4.6 + - - +
321B GLU* 2.9 38.4 + - + +
660B LEU 4.7 2.0 - - - -
661B THR* 4.0 36.1 - - + -
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Residues in contact with HIS 318 (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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177B ASP* 3.0 27.2 + - + +
178B THR* 3.6 17.9 - - + +
183B ARG* 3.8 19.0 + - - -
263B PRO* 2.7 36.5 + - + -
264B ARG 3.3 19.9 + - - -
265B SER* 3.7 11.9 - - - -
266B TYR* 3.7 37.4 + + + +
317B PHE* 1.3 84.1 - + - +
319B ARG* 1.3 65.9 + - - +
321B GLU* 3.7 5.0 - - + +
322B LEU* 3.0 25.8 + - - +
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Residues in contact with ARG 319 (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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129B ALA 5.5 0.2 + - - -
130B ARG* 3.3 42.6 - - - +
131B GLY 2.8 28.9 + - - +
132B SER* 3.0 29.0 + - - +
173B ALA* 4.3 5.1 + - - +
177B ASP* 2.9 15.2 + - - +
316B ASP 3.6 3.6 - - - +
318B HIS* 1.3 76.9 - - - +
320B ARG* 1.3 60.8 + - - +
322B LEU* 3.8 2.5 - - - +
323B TRP* 3.1 26.4 + - + +
382B PHE* 3.5 17.3 - - + -
227C TRP* 3.2 22.2 - - + +
228C ALA* 2.9 30.7 + - - +
229C ILE* 3.7 18.2 - - + -
231C GLN* 5.2 2.2 - - - +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASP* 2.8 42.9 + - - -
316B ASP* 2.8 17.1 + - - +
317B PHE* 3.7 6.7 - - - +
319B ARG* 1.3 74.3 - - - +
321B GLU* 1.3 59.1 + - - +
323B TRP* 3.2 1.6 + - - +
324B GLU* 2.9 60.3 + - - +
227C TRP* 3.8 26.7 - - + -
229C ILE* 3.5 33.4 - - + +
230C PRO* 4.9 5.3 - - - +
233C GLN* 5.7 2.6 + - - +
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Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 2.9 32.4 + - - +
265B SER* 3.3 22.0 + - - +
266B TYR 5.3 0.7 - - - +
267B ARG* 2.6 42.8 + - - +
317B PHE* 2.9 30.0 + - + +
318B HIS* 3.7 7.0 - - - +
319B ARG 3.4 0.2 - - - -
320B ARG* 1.3 76.0 - - - +
322B LEU* 1.3 59.9 + - - +
324B GLU* 4.2 5.3 - - - +
325B ALA* 2.9 33.9 + - - +
600B GLY 5.0 2.5 - - - +
602B VAL* 5.7 2.8 - - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 3.9 38.4 - - - +
133B ALA 4.1 13.2 - - - +
134B ALA* 4.7 1.3 - - + -
166B PHE* 4.0 26.7 - - + -
266B TYR* 4.4 7.9 - - + -
267B ARG* 4.8 7.6 - - + +
318B HIS 3.0 17.9 + - - +
319B ARG 3.8 3.4 - - - +
321B GLU* 1.3 80.4 - - - +
323B TRP* 1.3 63.5 + - - +
325B ALA* 3.4 4.2 + - - +
326B ILE* 3.2 34.6 + - + +
332B PRO* 3.7 29.8 - - + -
375B LEU* 4.9 1.8 - - + -
378B ASN* 5.2 0.7 - - - +
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Residues in contact with TRP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 3.7 11.6 - - + -
51B ALA 3.2 20.1 + - - -
133B ALA 5.2 3.4 - - - -
319B ARG* 3.1 17.9 + - + +
320B ARG 3.6 3.6 - - - +
322B LEU* 1.3 79.5 - - - +
324B GLU* 1.3 59.2 + - - +
326B ILE 3.4 0.5 + - - -
327B GLU* 2.9 51.5 + - - +
378B ASN* 3.0 43.2 + - + +
379B PRO* 3.4 39.7 - - + -
382B PHE* 5.6 2.2 - + - -
226C HIS* 3.2 44.9 - + + -
227C TRP* 3.4 36.3 - + + -
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Residues in contact with GLU 324 (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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43B THR 4.7 0.9 - - - +
45B PRO* 3.8 36.9 - - + +
46B GLY* 4.5 7.8 + - - -
50B THR* 4.1 27.4 - - + +
320B ARG* 2.9 44.5 + - - +
321B GLU* 4.2 4.5 + - - +
323B TRP* 1.3 73.3 - - - +
325B ALA* 1.3 61.8 + - - +
327B GLU* 3.7 7.4 - - + +
328B ALA* 2.9 31.2 + - - +
227C TRP* 4.1 6.1 - - + -
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Residues in contact with ALA 325 (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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45B PRO* 5.8 1.1 - - - -
267B ARG* 3.6 26.2 - - - +
321B GLU* 2.9 21.0 + - - +
322B LEU 3.7 4.5 - - - +
324B GLU* 1.3 75.1 - - - +
326B ILE* 1.3 59.5 + - - +
328B ALA* 3.2 1.6 + - - +
329B GLY 3.1 4.2 + - - -
330B ASP* 2.7 60.3 + - + +
332B PRO* 5.0 1.6 - - + -
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Residues in contact with ILE 326 (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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134B ALA* 3.4 33.4 - - + -
322B LEU* 3.2 18.4 + - + +
323B TRP 3.7 6.5 - - - +
325B ALA* 1.3 77.2 - - - +
327B GLU* 1.3 63.6 + - - +
329B GLY 3.0 10.7 + - - -
331B PHE* 3.5 15.9 - - - -
332B PRO* 3.5 24.5 - - + -
375B LEU* 3.7 15.3 - - + +
376B ASN* 3.6 7.4 - - - +
377B ARG* 3.6 26.7 - - - +
378B ASN* 3.6 20.9 - - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.3 11.1 - - - +
43B THR* 3.2 23.9 + - - +
48B GLN* 5.2 1.7 - - - +
49B PRO 4.5 1.6 - - - +
50B THR* 3.5 21.0 - - - +
51B ALA 3.0 24.4 + - - +
56B LYS* 3.8 40.0 + - + +
323B TRP* 2.9 46.0 + - - +
324B GLU* 3.3 8.1 + - - +
326B ILE* 1.3 75.9 - - + +
328B ALA* 1.3 56.1 + - - +
329B GLY 3.6 0.2 + - - -
378B ASN* 3.6 10.8 - - - +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PRO* 3.9 12.2 - - - +
43B THR 3.1 20.6 + - - +
44B PRO* 4.0 3.6 - - + -
45B PRO* 4.0 15.0 - - + -
324B GLU 2.9 18.0 + - - +
325B ALA 3.7 4.5 - - - +
327B GLU* 1.3 75.7 - - - +
329B GLY* 1.3 60.2 + - - +
330B ASP* 3.7 18.8 + - - +
599B LYS* 5.7 0.2 + - - -
629B HIS* 4.2 5.0 + - - +
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Residues in contact with GLY 329 (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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42B PRO* 4.4 7.2 - - - +
326B ILE 3.0 7.7 + - - -
327B GLU 3.3 1.0 + - - -
328B ALA* 1.3 79.4 - - - +
330B ASP* 1.3 57.6 + - - +
331B PHE* 3.1 40.8 + - - -
599B LYS* 3.5 11.6 + - - -
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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