Contacts of the helix formed by residues 268 - 281 (chain A) in PDB entry 1GPM
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 ASN 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ARG 3.3 1.8 + - - -
267A LEU* 1.3 94.6 + - - +
269A GLU* 1.3 63.1 + - - +
270A ALA 3.4 2.5 - - - -
271A GLU* 3.2 25.8 + - - +
272A GLN* 2.9 37.8 + - + +
131B ALA* 4.7 17.9 - - - +
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Residues in contact with GLU 269 (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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235A SER 4.3 12.3 - - - +
236A GLY 4.9 4.9 - - - +
259A PHE* 6.3 0.2 - - + -
265A LEU* 3.4 21.2 - - + +
266A ARG* 2.7 75.5 + - + +
267A LEU 2.9 5.3 + - - +
268A ASN* 1.3 75.8 - - - +
270A ALA* 1.3 64.6 + - - +
272A GLN* 3.2 12.0 + - - +
273A VAL* 3.0 39.2 + - + +
400A ARG* 4.8 3.5 + - - -
403A PHE* 4.2 4.9 - - - -
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Residues in contact with ALA 270 (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 PHE* 3.8 27.9 - - + -
261A ASP* 3.4 28.0 - - + +
265A LEU* 4.8 4.5 - - + +
266A ARG 4.6 1.2 + - - -
268A ASN 3.4 0.4 - - - -
269A GLU* 1.3 78.1 - - - +
271A GLU* 1.3 57.5 + - - +
273A VAL* 3.8 1.0 - - - +
274A LEU* 3.1 38.7 + - + +
287A HIS* 5.3 2.2 - - + +
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Residues in contact with GLU 271 (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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268A ASN* 3.2 26.2 + - - +
269A GLU 3.2 0.4 - - - -
270A ALA* 1.3 75.4 - - - +
272A GLN* 1.3 60.1 + - - +
274A LEU* 3.9 4.7 - - - +
275A ASP* 2.8 56.3 + - - +
131B ALA* 3.2 23.7 - - - +
132B ASP* 3.9 9.4 - - - +
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Residues in contact with GLN 272 (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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267A LEU 4.9 1.7 - - - +
268A ASN* 2.9 28.5 + - + +
269A GLU* 3.8 10.8 - - - +
271A GLU* 1.3 75.2 - - - +
273A VAL* 1.3 55.9 + - + +
275A ASP* 4.0 0.2 - - - +
276A MET* 2.8 38.0 + - - +
129B LEU* 3.6 34.2 + - + +
130B THR 3.2 28.9 + - - +
131B ALA* 3.8 12.0 - - - +
133B GLY* 4.3 6.4 - - - +
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 4.2 9.9 - - + -
235A SER 5.1 0.2 - - - +
236A GLY* 4.2 22.7 - - - -
259A PHE* 4.2 31.2 - - + -
269A GLU* 3.0 29.7 + - + +
270A ALA* 3.8 5.2 - - - +
272A GLN* 1.3 73.6 - - + +
274A LEU* 1.3 67.8 + - - +
276A MET* 4.7 4.3 - - - -
277A PHE* 2.9 51.2 + - + +
285A ILE* 5.5 0.4 - - + -
397A MET* 4.9 10.1 - - + -
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Residues in contact with LEU 274 (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 PHE* 4.3 11.2 - - + -
270A ALA* 3.1 21.0 + - + +
271A GLU* 3.9 4.9 - - - +
273A VAL* 1.3 81.0 - - - +
275A ASP* 1.3 64.5 + - - +
278A GLY* 2.9 31.2 + - - +
279A ASP* 3.6 2.9 + - - +
285A ILE* 4.1 25.1 - - + +
287A HIS* 3.2 59.0 - - + +
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A GLU* 2.8 39.8 + - - +
272A GLN 4.0 0.2 - - - +
274A LEU* 1.3 80.0 - - - +
276A MET* 1.3 62.3 + - - +
279A ASP* 3.1 25.9 + - + +
280A HIS* 2.9 25.5 + - - +
132B ASP* 3.1 47.2 - - - +
133B GLY* 3.9 2.4 - - - +
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Residues in contact with MET 276 (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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272A GLN 2.8 22.0 + - - +
273A VAL* 4.7 2.0 - - - -
275A ASP* 1.3 72.9 - - - +
277A PHE* 1.3 77.3 + - + +
280A HIS* 2.9 22.2 + - - +
281A PHE* 2.8 55.7 + - + -
393A LEU* 4.5 1.8 - - - -
394A PRO* 3.8 30.1 - - - -
397A MET* 3.6 32.3 - - + -
126B GLU* 4.9 0.2 - - - +
129B LEU* 3.9 21.3 - - + -
133B GLY* 4.1 6.8 - - - +
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Residues in contact with PHE 277 (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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234A LEU* 3.7 31.0 - - + -
236A GLY* 5.0 1.3 - - - -
241A SER* 3.6 35.2 - - - -
244A ALA* 4.8 0.4 - - + -
245A MET* 4.0 21.8 - - + -
273A VAL* 2.9 28.4 + - + +
276A MET* 1.3 99.1 - - + +
278A GLY* 1.3 57.4 + - - +
281A PHE* 3.6 15.1 + + - +
282A GLY 3.1 8.7 + - - -
283A LEU* 2.9 44.8 + - + +
285A ILE* 3.3 19.7 - - + -
393A LEU* 4.2 11.9 - - + -
397A MET* 4.6 4.0 - - + -
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Residues in contact with GLY 278 (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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274A LEU* 2.9 19.0 + - - -
277A PHE* 1.3 72.7 - - - +
279A ASP* 1.3 60.8 + - - +
282A GLY* 3.1 25.8 + - - -
283A LEU 3.6 16.4 - - - +
285A ILE* 3.6 8.5 - - - +
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Residues in contact with ASP 279 (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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274A LEU 3.6 2.3 + - - +
275A ASP* 3.1 31.6 + - + +
278A GLY* 1.3 78.4 - - - +
280A HIS* 1.3 67.5 + - - +
282A GLY* 4.1 2.9 + - - -
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Residues in contact with HIS 280 (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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275A ASP 2.9 10.2 + - - +
276A MET* 2.9 29.0 + - - +
279A ASP* 1.3 76.1 - - - +
281A PHE* 1.3 80.9 + + - +
126B GLU* 3.1 31.9 + - - -
133B GLY 4.2 11.9 + - - +
135B PRO* 4.2 20.4 - - + +
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Residues in contact with PHE 281 (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 MET* 3.7 25.1 - - + -
248A HIS* 3.6 17.7 + - + +
276A MET* 2.8 52.7 + - + -
277A PHE* 3.6 21.3 - + - +
280A HIS* 1.3 99.2 - + - +
282A GLY* 1.3 61.5 + - - +
283A LEU* 3.5 13.2 - - + -
391A LEU 4.7 2.0 - - - -
392A GLY* 3.7 28.5 - - - -
393A LEU* 4.1 11.7 - - + -
124B GLY* 6.4 0.4 - - - -
126B GLU* 4.1 2.0 - - - -
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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