Contacts of the helix formed by residues 208 - 214 (chain D) in PDB entry 4K9N
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 GLY 208 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D LEU* 1.3 74.5 - - - +
209D PRO* 1.3 74.5 - - - +
211D VAL* 3.2 19.1 + - - +
233D VAL* 5.3 2.7 - - - -
234D ALA* 4.3 3.1 - - - -
239D ARG 5.7 0.7 - - - -
241D PRO* 3.6 11.5 - - - +
273D ILE 2.9 11.5 + - - -
274D GLY 3.0 12.6 - - - -
275D ALA* 3.5 11.7 - - - +
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Residues in contact with PRO 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASN 5.2 6.5 - - - +
88D SER* 5.7 6.5 - - - +
89D HIS* 5.9 0.9 - - + +
208D GLY* 1.3 84.5 - - - +
210D ASP* 1.3 64.5 + - - +
211D VAL 3.0 1.3 - - - -
212D ASP* 3.1 4.8 + - + +
213D ALA* 3.0 23.1 + - - +
234D ALA* 5.6 1.6 - - + -
237D ALA* 5.7 1.3 - - + -
238D PRO* 3.7 41.1 - - + -
239D ARG* 3.6 35.1 - - + +
274D GLY 3.2 7.9 - - - +
275D ALA* 4.3 6.7 - - + -
276D PRO* 4.7 9.0 - - + -
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Residues in contact with ASP 210 (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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88D SER 4.5 3.5 - - - +
89D HIS* 2.8 46.3 + - - +
209D PRO* 1.3 81.9 - - - +
211D VAL* 1.3 60.6 + - - +
213D ALA* 3.8 12.2 - - + +
214D ALA* 3.0 28.8 + - - +
274D GLY* 3.1 28.5 + - - +
275D ALA* 5.1 0.3 - - - -
300D CYS* 3.7 14.6 + - - -
304D GLU* 4.2 6.4 - - - +
318D ILE* 3.8 16.2 - - + +
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Residues in contact with VAL 211 (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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207D LEU* 4.3 6.1 - - + -
208D GLY 3.2 8.9 + - - +
209D PRO 3.0 0.8 - - - -
210D ASP* 1.3 76.5 - - - +
212D ASP* 1.3 65.8 + - - +
214D ALA 3.2 1.6 + - - -
215D ASN 3.1 2.9 + - - -
216D ALA* 2.9 29.6 + - + +
217D ASN* 3.8 15.9 - - - +
220D CYS* 3.8 25.4 - - + -
241D PRO* 3.8 21.8 - - + +
273D ILE* 3.5 45.3 - - + +
274D GLY 4.3 0.4 + - - -
318D ILE* 3.9 10.1 - - + -
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Residues in contact with ASP 212 (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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62D ARG* 2.9 31.0 + - - -
208D GLY 4.1 0.8 + - - -
209D PRO 3.1 6.6 + - - +
211D VAL* 1.3 79.5 - - - +
213D ALA* 1.3 62.7 + - - +
215D ASN 3.0 4.2 + - - -
217D ASN* 3.0 21.8 + - - +
239D ARG* 2.7 42.6 + - + +
240D CYS 3.4 23.8 + - - +
241D PRO* 4.3 1.3 - - + +
393D GLY* 2.8 33.7 + - - -
394D SER 4.8 0.2 + - - -
395D TYR 4.8 0.3 - - - +
396D TYR* 4.3 1.6 + - - -
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Residues in contact with ALA 213 (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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62D ARG* 3.1 27.6 - - - +
88D SER 5.6 4.7 - - - +
89D HIS* 6.0 2.7 - - + +
151D GLN* 5.6 5.4 - - - +
209D PRO 3.0 14.7 + - - +
210D ASP* 3.9 15.7 - - + +
211D VAL 3.3 0.2 - - - -
212D ASP* 1.3 76.2 - - - +
214D ALA* 1.3 56.4 + - - +
215D ASN 3.2 0.2 - - - -
239D ARG* 3.5 27.5 - - - +
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Residues in contact with ALA 214 (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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62D ARG* 4.6 0.9 - - - -
210D ASP 3.0 18.9 + - - +
211D VAL 3.8 4.0 - - - +
212D ASP 3.1 0.2 - - - -
213D ALA* 1.3 75.8 - - - +
215D ASN* 1.3 70.4 + - - +
216D ALA* 3.3 5.4 + - + -
317D ASP* 5.6 2.0 - - - +
318D ILE* 4.2 4.0 - - + -
319D GLY* 3.7 32.5 - - - +
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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