Contacts of the helix formed by residues 208 - 214 (chain X) in PDB entry 3F6B
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207X LEU* 1.3 72.8 - - - +
209X PRO* 1.3 74.1 - - - +
211X VAL* 3.1 19.6 + - - +
233X VAL* 5.4 2.2 - - - -
234X ALA* 4.3 2.9 - - - -
239X ARG 5.7 0.7 - - - -
241X PRO* 3.6 10.8 - - - +
273X ILE 2.9 11.5 + - - -
274X GLY 3.1 13.7 - - - -
275X ALA* 3.6 11.9 - - - +
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Residues in contact with PRO 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87X ASN 5.3 7.0 - - - +
88X SER* 5.8 5.8 - - - +
89X HIS* 6.0 0.4 - - - +
208X GLY* 1.3 84.8 - - - +
210X ASP* 1.3 65.5 + - - +
211X VAL 3.1 0.9 - - - -
212X ASP* 3.1 4.8 + - + +
213X ALA* 3.0 23.5 + - - +
234X ALA* 5.6 1.6 - - + -
237X ALA* 5.8 0.9 - - - -
238X PRO* 3.7 38.6 - - + -
239X ARG* 3.6 36.2 - - + +
241X PRO* 5.4 0.2 - - + -
274X GLY 3.3 9.4 - - - +
275X ALA* 4.4 7.0 - - + -
276X PRO* 4.8 8.7 - - + -
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Residues in contact with ASP 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88X SER 4.5 3.3 - - - +
89X HIS* 2.8 47.4 + - - +
209X PRO* 1.3 79.2 - - - +
211X VAL* 1.4 64.9 + - - +
213X ALA* 3.8 12.6 - - + +
214X ALA* 3.0 24.3 + - - +
274X GLY* 3.1 27.5 + - - +
275X ALA* 5.0 0.2 - - - -
276X PRO* 5.7 0.3 - - - +
300X CYS* 3.7 14.4 + - - -
304X GLU* 4.2 6.4 - - - +
318X ILE* 3.8 18.0 - - + +
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Residues in contact with VAL 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X LEU* 4.2 7.6 - - + -
208X GLY 3.1 10.2 + - - +
209X PRO 3.1 0.8 - - - -
210X ASP* 1.4 78.1 - - - +
212X ASP* 1.4 65.1 + - - +
214X ALA 3.2 1.6 + - - -
215X ASN 3.1 2.9 + - - -
216X ALA* 3.0 32.0 + - + -
217X ASN* 3.8 16.2 - - - +
220X CYS* 3.8 15.9 - - - -
241X PRO* 3.7 26.5 - - + +
273X ILE* 3.4 44.0 - - + +
274X GLY 4.3 0.2 + - - -
318X ILE* 3.9 9.9 - - + -
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Residues in contact with ASP 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ARG* 2.9 35.4 + - - -
208X GLY 4.1 1.0 + - - -
209X PRO 3.1 6.2 + - - +
211X VAL* 1.4 79.9 - - - +
213X ALA* 1.3 59.4 + - - +
215X ASN 3.0 4.3 + - - -
217X ASN* 2.9 21.9 + - - +
239X ARG* 2.8 42.3 + - + +
240X CYS 3.4 22.8 + - - +
241X PRO* 4.3 0.8 - - + +
393X GLY* 2.8 34.1 + - - -
394X SER 4.7 0.2 + - - -
395X TYR 4.9 0.5 - - - +
396X TYR* 4.2 1.7 + - - -
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Residues in contact with ALA 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ARG* 3.1 28.6 - - - +
88X SER 5.6 3.8 - - - +
89X HIS* 6.1 2.0 - - + +
151X GLN* 5.6 6.3 - - - +
209X PRO 3.0 14.9 + - - +
210X ASP* 3.9 15.3 - - + +
212X ASP* 1.3 76.2 - - - +
214X ALA* 1.3 57.9 + - - +
239X ARG* 3.5 26.3 - - - +
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Residues in contact with ALA 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ARG* 4.4 0.9 - - - -
210X ASP 3.0 18.4 + - - +
211X VAL 3.7 4.3 - - - +
212X ASP 3.2 0.4 - - - -
213X ALA* 1.3 74.4 - - - +
215X ASN* 1.3 68.8 + - - +
216X ALA* 4.1 5.9 - - + +
317X ASP* 5.8 1.6 - - - +
318X ILE* 4.1 4.0 - - + -
319X GLY* 3.6 34.6 - - - +
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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