Contacts of the helix formed by residues 207 - 224 (chain B) in PDB entry 1I94
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 ALA 207 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 5.9 0.2 - - - +
38B GLY* 5.0 9.9 - - - +
76B GLN* 5.0 0.6 - - - +
204B ASN* 3.9 17.3 - - + -
206B ASP* 1.3 88.2 - - + +
208B ILE* 1.3 70.2 + - - +
209B ARG* 3.1 1.4 + - + -
210B SER* 3.2 15.0 + - - +
211B ILE* 3.2 6.7 + - - +
1001B WO2 2.8 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN* 4.1 19.8 + - - +
80B ILE* 5.7 1.8 - - - +
207B ALA* 1.3 69.1 - - - +
209B ARG* 1.3 62.2 - - - +
211B ILE* 2.8 27.4 - - - +
212B GLN* 2.9 8.2 + - - +
1001B WO2 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN 6.1 0.7 - - - +
207B ALA* 3.1 0.6 + - + -
208B ILE* 1.3 79.3 - - - +
210B SER* 1.3 64.8 + - - +
212B GLN* 3.1 7.4 + - - +
213B LEU* 2.8 23.7 + - - +
1001B WO2 3.7 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 4.7 9.1 + - - -
203B GLY* 5.4 2.0 - - - -
204B ASN* 4.0 35.0 - - - -
207B ALA* 3.2 14.6 + - - +
209B ARG* 1.3 75.7 - - - +
211B ILE* 1.3 54.8 + - - +
213B LEU* 2.8 8.8 + - - +
214B ILE* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN 4.7 8.7 - - - +
77B ALA* 5.3 5.8 - - + -
80B ILE* 5.2 10.1 - - + -
204B ASN 5.0 2.4 + - - +
205B ASP 5.8 2.5 - - - +
206B ASP 4.8 3.5 + - - +
207B ALA 3.2 5.8 + - - +
208B ILE* 2.8 21.2 + - - +
210B SER* 1.3 79.1 - - - +
212B GLN* 1.3 53.2 + - - +
214B ILE* 3.0 3.3 + - - -
215B LEU* 2.6 41.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 5.3 13.5 - - + +
208B ILE 2.9 9.2 + - - +
209B ARG* 3.6 10.3 - - - +
211B ILE* 1.3 76.8 - - - +
213B LEU* 1.3 56.0 + - - +
215B LEU* 4.8 3.8 - - - -
216B SER* 2.9 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ARG 2.8 13.9 + - - +
210B SER* 2.8 13.4 + - - +
212B GLN* 1.3 78.2 - - - +
214B ILE* 1.3 63.8 + - - +
216B SER* 4.2 1.9 - - - -
217B ARG* 3.8 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 5.5 12.6 - - + +
210B SER 2.6 18.6 + - - +
211B ILE* 4.0 2.2 - - - +
213B LEU* 1.3 75.4 - - - +
215B LEU* 1.3 64.8 + - - +
217B ARG* 3.8 3.0 + - - +
218B ALA* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE 5.2 5.6 - - - +
84B GLU* 4.2 16.2 - - + +
211B ILE* 2.6 26.3 + - + +
212B GLN* 4.6 2.9 - - - +
214B ILE* 1.3 75.1 - - - +
216B SER* 1.3 59.7 + - - +
218B ALA* 3.3 9.7 - - - +
219B VAL* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 4.9 4.9 - - - -
212B GLN 2.9 22.9 + - - -
213B LEU* 4.2 3.4 - - - -
215B LEU* 1.3 72.2 - - - +
217B ARG* 1.3 54.6 + - - +
218B ALA 2.9 1.1 - - - -
219B VAL* 2.5 30.6 + - - +
220B ASP* 2.6 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU 3.8 13.5 + - - +
214B ILE* 4.3 3.4 - - - +
216B SER* 1.3 77.4 - - - +
218B ALA* 1.3 54.7 + - - +
219B VAL 3.0 0.2 - - - -
220B ASP* 3.5 10.8 - - - -
221B LEU* 2.6 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 5.0 13.4 - - + +
214B ILE 3.3 14.7 + - - +
215B LEU* 3.3 15.7 - - - +
217B ARG* 1.3 79.0 - - - +
219B VAL* 1.3 59.4 + - - +
221B LEU* 4.2 5.0 - - - +
222B ILE* 3.9 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 4.0 27.1 - - + +
87B ARG* 5.5 4.7 - - + -
88B ALA* 4.1 17.3 - - + +
215B LEU 3.1 10.9 + - - +
216B SER* 2.5 21.4 + - - +
218B ALA* 1.3 73.4 - - - +
220B ASP* 1.3 61.4 + - - +
221B LEU 3.3 0.2 - - - -
222B ILE* 3.4 5.2 + - - +
223B ILE* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B SER 2.6 17.3 + - - +
217B ARG* 3.8 10.1 - - - +
219B VAL* 1.3 70.4 - - - +
221B LEU* 1.3 57.0 + - - +
223B ILE* 3.3 7.0 + - - +
224B GLN* 2.7 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 5.4 10.5 - - + +
58B ILE* 5.1 11.0 - - + -
59B GLU* 5.2 11.0 - - + +
217B ARG 2.6 23.4 + - - +
218B ALA* 4.4 6.3 - - - +
220B ASP* 1.3 71.4 - - - +
222B ILE* 1.3 66.3 + - - +
224B GLN* 3.6 6.6 + - - +
225B ALA* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.9 5.8 + - + +
62B ALA* 4.2 20.0 - - + -
88B ALA* 5.2 8.1 - - + -
218B ALA 3.9 10.7 + - - +
219B VAL* 3.4 12.3 + - - +
221B LEU* 1.3 77.2 - - - +
223B ILE* 1.3 55.4 + - - +
225B ALA* 2.4 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG 5.7 5.2 - - - +
88B ALA* 5.7 4.4 - - + +
219B VAL 3.1 10.1 + - - +
220B ASP* 3.5 11.0 - - - +
222B ILE* 1.3 79.2 - - - +
224B GLN* 1.3 58.8 + - - +
225B ALA* 2.8 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ASP* 2.7 22.2 + - + +
221B LEU* 3.6 7.4 - - - +
223B ILE* 1.3 70.0 - - - +
225B ALA* 1.3 64.2 + - - +
226B ARG 3.1 12.8 + - - +
227B GLY* 4.4 5.1 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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