Contacts of the helix formed by residues 290 - 299 (chain C) 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 ALA 290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C VAL* 4.1 9.6 - - + -
261C ASP 2.9 15.8 + - - +
288C VAL* 3.3 6.9 + - + +
289C PRO* 1.3 75.3 - - - +
291C GLU* 1.3 67.7 + - - +
292C ASP 3.3 2.0 - - - -
293C ARG* 3.3 11.1 + - + +
294C PHE* 3.0 44.9 + - + -
318C VAL* 4.4 15.5 - - + -
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ASP* 3.2 5.9 + - - +
262C ASN 3.7 10.3 - - - -
263C GLY* 3.8 33.5 - - - +
289C PRO 3.9 0.6 - - - -
290C ALA* 1.3 77.1 - - - +
292C ASP* 1.3 67.0 + - - +
294C PHE* 3.2 1.6 + - - +
295C LEU* 2.9 44.6 + - + +
418C LYS* 2.9 49.1 + - - +
421C CYS* 5.7 0.7 - - - +
425C ARG* 4.6 3.5 + - - -
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Residues in contact with ASP 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C ALA 3.3 0.2 - - - -
291C GLU* 1.3 85.1 - - - +
293C ARG* 1.3 60.7 + - - +
295C LEU* 4.6 6.5 - - - +
296C SER* 2.8 34.9 + - - +
418C LYS* 6.0 1.7 - - - +
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C ALA* 3.3 17.0 + - + +
292C ASP* 1.3 77.3 - - - +
294C PHE* 1.3 61.7 + - - +
296C SER* 3.9 5.0 - - - -
297C ALA* 3.2 23.4 + - + +
314C VAL* 4.0 11.8 - - + +
317C GLU* 2.9 38.0 + - - +
318C VAL* 3.5 31.4 - - - +
321C GLU* 2.7 41.6 + - - -
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Residues in contact with PHE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C VAL* 4.1 10.5 - - + -
262C ASN* 3.5 40.6 - - + +
264C LEU* 4.5 4.9 - - + -
290C ALA* 3.0 42.6 + - + +
291C GLU 3.6 3.1 - - - +
293C ARG* 1.3 73.9 - - - +
295C LEU* 1.3 60.9 + - + +
297C ALA* 3.3 4.8 + - - +
298C LEU* 2.9 39.9 + - + +
310C ILE* 5.0 0.6 - - + +
311C ILE* 3.3 46.4 - - + -
314C VAL* 3.8 23.8 - - + -
315C PHE* 3.8 28.0 - + + -
318C VAL* 4.6 2.5 - - + -
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ASN 5.3 0.9 - - - +
263C GLY 5.7 1.1 - - - +
264C LEU* 4.6 9.6 - - + -
291C GLU* 2.9 43.2 + - + +
292C ASP* 4.2 7.2 - - - +
294C PHE* 1.3 74.0 - - + +
296C SER* 1.3 60.9 + - - +
298C LEU* 3.5 8.4 - - + +
299C ALA* 2.8 30.3 + - - +
416C VAL* 3.8 38.7 - - + +
417C LYS* 4.6 0.4 - - - -
418C LYS* 3.7 36.1 - - + +
421C CYS* 4.8 3.4 - - - -
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ASP* 2.8 26.1 + - - +
293C ARG* 3.9 5.4 - - - -
295C LEU* 1.3 77.3 - - - +
297C ALA* 1.3 62.4 + - - +
298C LEU 3.2 0.9 + - - -
299C ALA* 3.3 19.8 + - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C ARG* 3.2 16.0 + - + +
294C PHE 3.6 4.7 - - - +
295C LEU 3.2 0.2 - - - -
296C SER* 1.3 78.2 - - - +
298C LEU* 1.3 58.6 + - - +
299C ALA 3.5 2.1 - - - +
301C GLU* 5.1 0.3 - - - +
310C ILE* 3.3 36.5 - - + +
313C ARG* 4.7 10.4 + - - +
314C VAL* 3.9 16.2 - - + -
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C LEU* 4.2 15.7 - - + -
294C PHE* 2.9 28.1 + - + +
295C LEU* 3.0 8.7 + - + +
297C ALA* 1.3 81.1 - - - +
299C ALA* 1.3 64.8 + - - +
300C GLY 3.3 0.5 + - - -
301C GLU* 3.0 23.0 + - - +
307C LYS* 4.1 24.6 - - + +
310C ILE* 3.9 22.9 - - + -
311C ILE* 3.8 34.5 - - + -
415C GLU* 4.4 3.8 - - - +
416C VAL* 4.2 36.2 + - + +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C LEU 2.8 10.2 + - - +
296C SER* 3.3 19.4 + - - +
297C ALA 4.8 1.7 - - - +
298C LEU* 1.3 77.6 - - - +
300C GLY* 1.3 59.0 + - - +
301C GLU* 3.2 5.7 + - - +
415C GLU* 3.8 10.1 - - - +
416C VAL 5.1 2.5 - - - -
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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