Contacts of the helix formed by residues 303 - 309 (chain D) in PDB entry 4XH9
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 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D TYR* 4.7 0.9 - - - -
274D LYS* 5.7 0.7 + - - -
294D LEU* 3.8 21.8 - - + +
301D LYS 4.0 0.4 + - - -
302D LEU* 1.3 76.7 - - - +
304D LEU* 1.3 68.4 + - - +
305D TRP* 3.7 18.7 - - - +
306D SER* 3.1 29.2 + - - -
307D PHE* 3.4 7.8 - - - -
7E LYS* 6.0 1.6 - - - +
58E TRP* 4.1 10.5 + - - -
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Residues in contact with LEU 304 (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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196D ALA* 5.7 0.2 - - + -
200D TYR* 3.7 42.0 - - + -
204D MET* 4.3 17.9 - - + -
210D MET* 5.6 0.2 - - + -
218D ILE* 5.1 0.9 - - + -
219D PHE* 3.9 17.9 - - + -
277D LEU* 4.1 25.8 - - + -
290D LEU* 4.0 33.0 - - + +
303D ASP* 1.3 74.0 - - - +
305D TRP* 1.3 64.3 + - - +
307D PHE* 2.9 18.2 + - + +
308D LEU* 2.9 29.8 + - + +
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Residues in contact with TRP 305 (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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270D GLN* 3.4 49.6 - - + -
273D ALA* 4.9 1.6 - - + -
274D LYS* 3.6 63.8 - - + +
277D LEU* 4.1 9.3 - - + +
303D ASP* 3.2 15.5 - - - +
304D LEU* 1.3 78.5 - - - +
306D SER* 1.3 55.9 + - - +
308D LEU* 3.2 25.1 + - + +
309D ASP* 2.9 30.0 + - + +
7E LYS* 4.4 8.9 - - - +
58E TRP* 3.6 30.6 - + - -
72E LEU* 3.8 32.8 + - + -
75E PRO* 5.2 3.8 - - + +
76E ASP* 5.4 0.2 - - - -
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Residues in contact with SER 306 (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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302D LEU* 3.7 23.1 - - - +
303D ASP* 3.1 27.7 + - - -
305D TRP* 1.3 77.6 - - - +
307D PHE* 1.3 60.5 + - - +
309D ASP* 3.2 11.5 + - - +
310D ILE* 3.4 19.0 + - - +
41E ASN* 3.0 34.6 + - - +
58E TRP* 3.8 14.5 - - - -
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Residues in contact with PHE 307 (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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192D ASP* 3.8 43.1 - - + -
193D LEU* 4.8 1.0 - - - +
195D LEU* 3.7 26.7 - - + -
196D ALA* 4.1 15.8 - - + +
200D TYR* 3.5 28.3 - + - -
222D LEU* 3.9 11.3 - - - +
298D PHE 4.3 2.7 - - - -
299D SER* 3.7 27.6 - - - -
300D ARG* 4.4 9.6 - - - -
302D LEU* 3.9 15.3 - - + -
303D ASP 3.4 12.1 - - - -
304D LEU* 2.9 12.6 + - + +
306D SER* 1.3 76.7 - - - +
308D LEU* 1.3 62.2 + - - +
310D ILE* 3.1 28.7 + - + +
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Residues in contact with LEU 308 (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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218D ILE* 3.6 34.1 - - + +
219D PHE* 3.9 22.9 - - + -
222D LEU* 3.9 18.4 - - + -
266D TYR* 2.5 43.9 + - - +
270D GLN* 4.0 5.5 + - + -
273D ALA* 5.3 1.8 - - + -
277D LEU* 3.6 23.1 - - + -
304D LEU* 2.9 25.1 + - + +
305D TRP* 3.2 24.9 + - + +
307D PHE* 1.3 75.9 - - - +
309D ASP* 1.3 58.6 + - - +
310D ILE 3.2 1.8 + - - -
311D PRO* 3.6 1.1 - - - +
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Residues in contact with ASP 309 (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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270D GLN* 2.7 24.1 + - - +
305D TRP* 2.9 21.1 + - + +
306D SER 3.2 6.7 + - - +
307D PHE 3.2 0.6 - - - -
308D LEU* 1.3 76.4 - - - +
310D ILE* 1.3 63.6 + - - +
311D PRO 3.4 2.9 - - - -
312D ARG* 2.6 51.1 + - - +
313D SER* 3.0 27.3 + - - -
41E ASN* 5.1 1.2 + - - +
58E TRP* 3.5 22.2 - - + -
72E LEU* 4.8 0.4 - - - +
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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