Contacts of the helix formed by residues 270 - 278 (chain D) in PDB entry 4G5O
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 LYS 270 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLU* 3.0 33.2 + - - +
44D SER 4.7 0.2 - - - -
150D ASP* 2.6 28.2 + - - +
226D ALA* 4.1 13.1 - - + +
227D LEU* 4.3 2.9 - - - +
228D SER* 3.4 25.7 - - - +
229D ASP* 5.5 1.8 + - - -
269D ASN* 1.3 101.1 + - - +
271D LYS* 1.3 65.1 + - - +
272D ASP* 3.1 5.0 + - - -
273D LEU* 3.1 11.8 + - + -
274D PHE* 3.1 21.3 + - - +
401D GDP 3.0 55.4 + - + -
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C GLU* 4.7 1.4 + - - -
297C GLU* 4.1 2.5 + - - +
227D LEU* 4.0 19.5 - - + -
268D LEU 4.4 2.0 - - - +
269D ASN 3.1 2.6 - - - -
270D LYS* 1.3 76.7 - - - +
272D ASP* 1.3 65.5 + - - +
274D PHE* 3.7 3.3 - - - +
275D GLU* 3.1 23.4 + - - +
296D TYR* 3.7 27.5 - - + +
323D PHE* 3.2 22.6 + - + +
324D THR 3.3 12.0 + - - +
325D CYS* 4.1 17.9 - - + +
331D ASN* 3.2 8.7 - - - +
402D CIT 2.9 51.7 + - - -
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ARG* 5.2 0.5 + - - -
270D LYS 3.6 2.3 - - - -
271D LYS* 1.3 78.8 - - + +
273D LEU* 1.3 72.1 + - - +
275D GLU* 3.3 16.6 + - - +
276D GLU* 3.3 15.2 + - - +
325D CYS* 3.5 20.5 - - + -
401D GDP 2.8 46.5 + - - +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ASP* 3.6 35.0 - - + +
228D SER* 3.8 14.1 - - - +
270D LYS* 3.1 16.1 + - + +
272D ASP* 1.3 77.2 - - - +
274D PHE* 1.3 60.3 + - - +
276D GLU* 3.1 7.7 + - + +
277D LYS* 2.9 39.0 + - + +
401D GDP 3.4 36.1 - - + +
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU* 3.4 37.7 - - + -
228D SER* 4.2 5.7 - - - +
230D TYR* 3.6 30.3 - + - -
270D LYS 3.1 14.7 + - - +
271D LYS* 3.7 6.1 - - - +
272D ASP 3.3 0.2 - - - -
273D LEU* 1.3 77.5 - - - +
275D GLU* 1.3 62.0 + - - +
277D LYS* 3.4 3.7 + - - +
278D ILE* 3.0 46.3 + - + +
283D LEU* 4.4 2.0 - - + -
296D TYR* 3.6 25.1 - + - -
299D ALA* 3.8 20.9 - - + -
300D ALA* 4.0 13.0 - - - -
303D ILE* 3.5 31.6 - - + -
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C LYS* 5.0 1.9 + - - -
402C CIT 2.7 36.4 - - - +
271D LYS 3.1 13.8 + - - +
272D ASP* 3.5 12.6 - - - +
273D LEU 3.2 0.2 - - - -
274D PHE* 1.3 78.0 - - - +
276D GLU* 1.3 62.4 + - + +
278D ILE* 3.3 17.9 - - - +
279D LYS* 3.7 13.3 - - - +
296D TYR* 3.3 40.8 - - + -
297D GLU* 5.9 0.4 - - - -
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D ASP 3.3 9.5 + - - +
273D LEU* 3.1 12.1 + - + +
275D GLU* 1.3 80.8 - - + +
277D LYS* 1.3 65.8 + - + +
279D LYS* 3.1 54.0 + - - +
280D ARG* 4.3 12.9 + - - -
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D SER* 5.5 6.8 + - - -
144D ARG* 5.1 5.7 - - - +
228D SER* 3.0 33.5 + - - +
230D TYR* 3.1 20.0 + - + +
231D ASP* 2.7 40.8 + - - +
232D LEU* 5.5 4.6 - - - +
273D LEU* 2.9 22.9 + - + +
274D PHE 3.9 1.1 - - - +
276D GLU* 1.3 73.2 - - + +
278D ILE* 1.3 57.6 + - - +
279D LYS 2.9 8.7 + - - -
280D ARG* 3.0 13.8 + - + +
281D SER* 2.8 26.0 + - - -
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Residues in contact with ILE 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C CIT 5.0 3.4 - - + +
230D TYR* 3.2 22.6 + - + +
274D PHE* 3.0 42.6 + - + +
275D GLU 3.3 17.3 - - - +
277D LYS* 1.3 76.5 - - - +
279D LYS* 1.3 62.6 + - + +
280D ARG 3.3 0.7 + - - -
281D SER 3.9 13.1 + - - +
283D LEU* 4.3 10.5 - - + +
294D ASN* 3.8 26.0 - - - +
295D THR 4.3 5.4 - - - +
296D TYR* 3.8 29.8 - - + +
299D ALA* 3.9 19.5 - - + -
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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