Contacts of the helix formed by residues 316 - 328 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ARG* 2.8 29.9 + - - +
177A ASP* 3.1 9.0 - - - -
314A ASP* 2.9 13.0 + - - +
315A PRO* 1.3 79.5 - - - +
317A PHE* 1.3 56.7 + - - +
319A ARG* 3.2 2.8 + - + +
320A ARG* 2.8 28.7 + - - +
228D ALA 4.4 2.8 - - - +
229D ILE* 3.7 31.6 - - + +
230D PRO* 3.2 11.1 - - - +
231D GLN* 2.8 37.0 + - - +
233D GLN* 4.1 6.6 + - - -
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Residues in contact with PHE 317 (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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177A ASP* 3.5 0.6 + - - -
178A THR* 3.9 13.0 - - + -
264A ARG* 3.6 44.9 - - - -
302A LEU* 5.2 2.5 - - + -
310A LEU* 3.8 30.5 - - + -
314A ASP* 3.2 34.2 + - - +
315A PRO 3.4 1.8 - - - -
316A ASP* 1.3 76.7 - - - +
318A HIS* 1.3 70.9 + + - +
320A ARG* 3.7 4.3 - - - +
321A GLU* 2.9 40.3 + - + +
602A VAL* 6.4 0.2 - - + -
660A LEU 4.7 1.6 - - - -
661A THR* 3.8 39.0 - - + -
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Residues in contact with HIS 318 (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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177A ASP* 2.9 29.2 + - + +
178A THR* 3.7 19.0 - - + +
183A ARG* 3.8 19.0 + - - -
263A PRO* 2.8 37.5 + - + -
264A ARG 3.3 20.3 + - - -
265A SER* 3.8 11.4 - - - -
266A TYR* 3.6 37.3 + + + +
302A LEU* 4.7 0.2 - - - +
317A PHE* 1.3 81.2 - + - +
319A ARG* 1.3 60.8 + - - +
321A GLU* 3.8 4.6 - - + +
322A LEU* 2.9 31.9 + - - +
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Residues in contact with ARG 319 (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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129A ALA 5.5 0.4 + - - -
130A ARG* 3.3 42.4 - - - +
131A GLY 2.8 28.5 + - - +
132A SER* 3.1 32.1 + - - +
173A ALA* 4.3 5.5 + - - +
177A ASP* 2.8 15.4 + - - +
316A ASP 3.6 4.0 - - - +
318A HIS* 1.3 76.0 - - - +
320A ARG* 1.3 62.2 + - - +
322A LEU* 3.8 3.3 - - - +
323A TRP* 3.1 26.0 + - + +
382A PHE* 3.4 18.6 - - + -
227D TRP* 3.1 23.6 - - + +
228D ALA* 2.9 35.2 + - - +
229D ILE* 3.8 13.0 - - + -
231D GLN* 5.1 2.4 - - - +
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Residues in contact with ARG 320 (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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314A ASP* 2.9 40.9 + - - -
316A ASP* 2.8 16.8 + - - +
317A PHE* 3.7 7.2 - - - +
319A ARG* 1.3 75.0 - - - +
321A GLU* 1.3 61.4 + - - +
323A TRP* 3.2 2.8 + - - +
324A GLU* 2.8 61.1 + - - +
227D TRP* 3.8 26.9 - - + -
229D ILE* 3.5 34.7 - - + +
230D PRO* 5.0 4.6 - - - +
233D GLN* 5.8 1.8 + - - +
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Residues in contact with GLU 321 (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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264A ARG* 3.3 27.1 + - - +
265A SER* 2.7 25.7 + - - -
266A TYR 4.6 1.6 + - - -
267A ARG* 2.6 41.4 + - - +
317A PHE* 2.9 31.7 + - + +
318A HIS* 3.8 6.1 - - - +
320A ARG* 1.3 77.2 - - - +
322A LEU* 1.3 63.1 + - - +
324A GLU* 3.9 7.0 - - - +
325A ALA* 2.9 26.6 + - - +
600A GLY 4.8 1.9 - - - +
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Residues in contact with LEU 322 (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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132A SER* 3.9 38.6 - - - +
133A ALA 4.2 13.0 - - - +
134A ALA* 4.8 2.9 - - + -
166A PHE* 4.1 26.5 - - + -
266A TYR* 4.5 8.5 - - + +
267A ARG* 4.9 5.8 - - + +
318A HIS 2.9 17.0 + - - +
319A ARG 3.8 2.9 - - - +
321A GLU* 1.3 82.1 + - - +
323A TRP* 1.3 64.4 + - + +
325A ALA* 3.3 5.8 + - - +
326A ILE* 3.1 35.5 + - + +
332A PRO* 3.6 29.2 - - + -
375A LEU* 5.1 0.2 - - + -
378A ASN* 5.1 0.9 - - - +
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Residues in contact with TRP 323 (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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50A THR* 3.7 19.4 - - + -
51A ALA 3.3 18.9 + - - -
133A ALA 5.0 3.8 - - - -
319A ARG* 3.1 18.0 + - + +
320A ARG 3.2 3.8 + - - +
322A LEU* 1.3 81.4 - - + +
324A GLU* 1.3 57.7 + - - +
326A ILE 3.3 0.2 + - - -
327A GLU* 3.0 51.7 + - - +
378A ASN* 3.0 50.2 + - + +
379A PRO* 3.4 40.2 - - + -
382A PHE* 5.5 3.4 - + - -
226D HIS* 3.1 39.7 - + + -
227D TRP* 3.4 33.4 - + + -
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Residues in contact with GLU 324 (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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43A THR 4.7 0.7 - - - +
45A PRO* 3.7 39.1 - - + +
46A GLY* 4.3 9.0 + - - +
50A THR* 4.2 25.9 - - + +
320A ARG* 2.8 50.9 + - + +
321A GLU* 4.0 5.5 + - - +
323A TRP* 1.3 69.6 - - - +
325A ALA* 1.3 59.7 + - - +
327A GLU* 3.2 7.6 + - + +
328A ALA* 2.8 31.9 + - - +
227D TRP* 4.2 4.3 - - + -
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Residues in contact with ALA 325 (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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45A PRO* 5.4 1.5 - - - +
267A ARG* 3.6 26.0 - - - +
321A GLU* 2.9 18.8 + - - +
322A LEU 3.5 4.7 - - - +
324A GLU* 1.3 75.1 - - - +
326A ILE* 1.3 65.5 + - + +
328A ALA* 3.2 2.0 + - - +
329A GLY 3.1 4.0 + - - -
330A ASP* 2.8 57.1 + - + +
332A PRO* 5.0 0.4 - - + -
600A GLY* 6.4 0.2 - - - -
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Residues in contact with ILE 326 (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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134A ALA* 3.4 32.5 - - + -
322A LEU* 3.1 18.5 + - + +
323A TRP 3.7 7.0 - - - +
325A ALA* 1.3 74.9 - - - +
327A GLU* 1.3 65.1 + - - +
329A GLY 3.1 10.6 + - - -
331A PHE* 3.6 15.2 - - - -
332A PRO* 3.4 26.0 - - + -
375A LEU* 3.7 13.7 - - + +
376A ASN* 3.7 8.2 - - - +
377A ARG* 3.7 27.4 - - + +
378A ASN* 3.6 21.1 - - - +
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Residues in contact with GLU 327 (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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42A PRO* 3.2 24.8 - - - +
43A THR* 3.3 10.4 + - - +
48A GLN* 5.0 2.4 - - - +
49A PRO 4.4 2.1 - - - +
50A THR* 3.5 22.5 - - - +
51A ALA 3.0 23.8 + - - +
56A LYS* 3.8 40.6 + - + +
323A TRP* 3.0 44.6 + - - +
324A GLU* 3.2 7.3 + - + +
326A ILE* 1.3 76.9 - - + +
328A ALA* 1.3 57.4 + - - +
329A GLY 3.6 0.3 + - - -
378A ASN* 3.6 10.7 + - - +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 3.8 13.0 - - - +
43A THR 3.2 20.3 + - - +
44A PRO* 4.2 3.8 - - + -
45A PRO* 4.2 2.2 - - + -
324A GLU 2.8 17.0 + - - +
325A ALA 3.6 4.7 - - - +
326A ILE 3.2 0.2 - - - -
327A GLU* 1.3 78.3 - - - +
329A GLY* 1.3 57.7 + - - +
330A ASP* 3.7 20.1 + - - +
629A HIS* 4.0 18.4 - - + +
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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