Contacts of the helix formed by residues 380 - 391 (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 PHE 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C GLN* 3.8 23.3 - - + -
24C ALA* 3.7 31.2 - - + -
25C ARG* 3.6 27.4 - - + -
28C ARG* 3.9 24.2 - - + -
34C CYS* 5.2 0.4 - - - -
36C LEU* 5.0 0.9 - - + -
338C TYR* 3.5 32.8 - + - -
339C PRO* 3.9 17.9 - - + -
342C ILE* 4.1 10.8 - - + -
379C LEU* 1.3 75.9 - - - +
381C LYS* 1.3 67.0 + - - +
382C ASP* 3.3 16.8 - - - +
383C GLU* 2.9 33.1 + - + +
384C VAL* 3.0 12.3 + - - +
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Residues in contact with LYS 381 (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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25C ARG* 5.7 0.4 - - - +
238C VAL* 4.0 17.7 - - + -
239C ASP* 2.8 26.1 + - - +
337C ILE* 3.7 21.3 - - + +
339C PRO* 5.1 2.4 - - + +
379C LEU 4.2 0.2 + - - -
380C PHE* 1.3 73.8 - - - +
382C ASP* 1.3 58.2 + - - +
384C VAL* 3.2 9.1 + - + +
385C ARG* 3.0 61.9 + - - +
526C POP 2.5 32.7 + - - -
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Residues in contact with ASP 382 (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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25C ARG* 2.9 40.8 + - - +
29C GLU* 4.6 8.6 - - - +
380C PHE* 3.4 18.2 - - - +
381C LYS* 1.3 74.7 - - - +
383C GLU* 1.3 72.7 + - - +
385C ARG* 3.5 18.0 + - - +
386C LYS* 3.1 40.6 + - - +
399C TYR* 4.7 2.5 + - + -
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Residues in contact with GLU 383 (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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25C ARG* 6.4 0.2 - - + -
28C ARG* 2.8 43.4 + - + +
208C TRP* 2.7 33.1 + - - -
213C ILE* 4.0 7.5 - - + +
379C LEU* 3.5 15.7 - - + -
380C PHE* 2.9 29.7 + - + +
382C ASP* 1.3 88.6 + - - +
384C VAL* 1.3 66.4 + - - +
386C LYS* 3.2 16.0 + - + +
387C ILE* 2.9 29.0 + - + +
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Residues in contact with VAL 384 (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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238C VAL* 3.8 17.3 - - + +
239C ASP* 4.0 9.2 - - - +
242C VAL* 3.7 31.0 - - + +
337C ILE* 3.8 26.0 - - + -
376C LEU* 4.1 12.3 - - + -
379C LEU* 3.9 17.5 - - + -
380C PHE 3.0 16.6 + - - +
381C LYS* 3.5 10.5 - - + +
383C GLU* 1.3 77.6 - - - +
385C ARG* 1.3 56.5 + - - +
387C ILE* 3.1 11.0 - - - +
388C GLY 2.9 23.9 + - - -
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Residues in contact with ARG 385 (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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238C VAL* 4.6 10.7 - - + +
381C LYS* 3.0 55.9 + - - +
382C ASP* 3.7 14.4 - - - +
383C GLU 3.2 0.2 - - - -
384C VAL* 1.3 75.7 - - - +
386C LYS* 1.3 62.3 + - - +
388C GLY* 3.0 10.9 + - - -
389C LEU* 3.1 13.7 + - - +
398C LEU* 2.9 45.5 + - + +
399C TYR* 3.5 46.0 - - + +
400C ARG 4.6 10.7 + - - -
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Residues in contact with LYS 386 (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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29C GLU* 4.1 28.5 - - - +
210C PRO* 4.2 25.2 - - + +
382C ASP* 3.1 29.4 + - - +
383C GLU* 3.2 14.8 + - + +
385C ARG* 1.3 76.2 - - - +
387C ILE* 1.3 61.8 + - - +
389C LEU* 3.6 7.9 + - + +
390C GLU* 3.4 24.3 + - - +
399C TYR* 4.1 13.5 - - - +
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Residues in contact with ILE 387 (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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210C PRO* 4.0 33.0 - - + +
213C ILE* 4.7 15.3 - - + -
214C ILE* 4.1 13.2 - - + -
242C VAL* 3.5 21.8 - - + -
246C LEU* 4.2 13.2 - - + -
376C LEU* 4.0 8.5 - - + -
379C LEU* 3.6 25.4 - - + -
383C GLU* 2.9 19.6 + - - +
384C VAL* 3.1 15.3 - - - +
386C LYS* 1.3 73.6 - - - +
388C GLY* 1.3 65.3 + - - +
390C GLU* 3.2 6.7 + - - +
391C LEU* 2.9 30.2 + - + +
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Residues in contact with GLY 388 (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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242C VAL* 3.8 20.0 - - - -
384C VAL 2.9 15.0 + - - -
385C ARG 3.0 4.6 + - - -
387C ILE* 1.3 77.0 - - - +
389C LEU* 1.3 61.4 + - - +
391C LEU* 3.0 16.5 + - - +
392C GLY 3.1 8.5 + - - -
393C LEU* 3.1 13.8 + - - +
398C LEU* 3.6 12.1 - - - -
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Residues in contact with LEU 389 (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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385C ARG 3.1 12.9 + - - +
386C LYS* 3.9 9.6 - - + +
388C GLY* 1.3 71.4 - - - +
390C GLU* 1.3 62.9 + - - +
392C GLY* 2.8 17.2 + - - -
393C LEU 3.7 17.9 - - - +
395C TYR* 4.0 23.6 - - + -
398C LEU* 3.4 11.3 - - + +
399C TYR* 4.2 22.2 - - + +
189D GLN* 3.8 31.9 - - + +
192D ARG* 3.1 28.6 + - - +
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Residues in contact with GLU 390 (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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210C PRO* 4.2 18.2 - - + +
211C ALA* 5.1 7.8 + - + +
214C ILE* 3.8 22.7 - - + -
249C ARG* 5.3 3.3 + - - -
386C LYS 3.4 11.1 + - - +
387C ILE* 3.2 9.3 + - - +
389C LEU* 1.3 80.2 - - - +
391C LEU* 1.3 59.2 + - - +
392C GLY* 3.3 3.5 + - - -
124D GLY* 5.7 1.6 - - - -
192D ARG* 3.7 24.6 + - - +
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Residues in contact with LEU 391 (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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214C ILE* 4.3 20.2 - - + -
242C VAL* 4.2 15.7 - - + +
245C MET* 3.7 53.4 - - + +
246C LEU* 4.1 25.6 - - + +
249C ARG* 3.6 33.0 - - - +
281C PHE* 4.6 2.4 - - - -
387C ILE* 2.9 20.7 + - + +
388C GLY* 3.0 11.2 + - - +
390C GLU* 1.3 78.7 - - - +
392C GLY* 1.3 58.8 + - - +
393C LEU* 3.6 0.6 + - - -
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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