Contacts of the helix formed by residues 213 - 223 (chain B) in PDB entry 3IFS
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 THR 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.7 23.6 - - + -
201B ILE* 4.7 1.2 - - - +
202B PRO* 3.7 29.2 - - + +
205B VAL* 4.0 17.7 - - + -
210B SER* 2.7 22.1 + - - +
211B VAL 3.3 0.2 - - - +
212B LEU* 1.3 82.8 - - - +
214B PRO* 1.4 78.0 - - - +
215B VAL* 3.0 20.5 + - - +
216B GLY 3.2 2.8 + - - -
217B LEU* 3.2 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.3 33.9 - - - +
63B ILE* 3.8 24.9 - - + -
141B ASN* 5.1 0.7 - - - +
179B THR* 4.0 9.5 + - + +
199B PHE* 3.7 22.7 - - + -
200B VAL 3.3 20.4 - - - +
202B PRO* 5.1 1.1 - - + -
213B THR* 1.4 90.5 - - - +
215B VAL* 1.3 61.8 + - - +
217B LEU* 3.7 3.6 - - + -
218B LEU* 3.2 25.8 + - + +
219B PRO* 4.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY 3.5 24.7 - - - +
85B SER* 3.7 17.9 - - - +
88B GLY* 6.5 0.4 - - - -
89B ALA* 4.3 6.5 - - + +
143B ILE* 3.6 24.3 - - + +
179B THR* 3.9 6.6 - - + +
201B ILE* 3.5 35.7 - - + -
210B SER* 3.5 19.5 - - - +
211B VAL* 4.9 1.3 - - - -
213B THR* 3.0 16.8 + - - +
214B PRO* 1.3 79.0 - - - +
216B GLY* 1.3 60.5 + - - +
219B PRO* 3.6 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 4.2 11.4 - - - +
211B VAL* 3.1 20.7 + - - -
213B THR 3.2 4.4 + - - -
215B VAL* 1.3 82.8 - - - +
217B LEU* 1.3 64.4 + - - +
218B LEU 3.4 0.7 - - - -
219B PRO* 3.4 4.0 - - - +
220B ILE* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 5.9 2.0 - - + -
60B PHE* 3.7 32.1 - - + -
63B ILE* 4.0 21.0 - - + +
211B VAL 4.4 5.6 - - - +
212B LEU* 3.6 22.0 - - - +
213B THR 3.2 18.4 + - - +
214B PRO* 3.4 0.9 + - + -
216B GLY* 1.3 76.8 - - - +
218B LEU* 1.3 62.4 + - - +
220B ILE* 4.3 2.7 - - - -
221B ALA* 3.0 26.5 + - - +
227B ILE* 3.8 26.1 - - + +
230B MSE 4.4 17.7 - - - -
231B MSE 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.7 37.1 - - + +
66B CYS* 4.2 7.0 - - + -
67B ALA* 4.1 12.3 - - - +
70B ILE* 4.4 6.1 - - + -
77B LEU* 5.6 0.7 - - + -
141B ASN* 3.6 29.2 - - + +
177B TYR* 4.0 17.0 - - + -
179B THR* 4.9 1.6 - - - +
199B PHE* 3.9 25.8 - - + -
214B PRO* 3.2 12.6 + - + +
217B LEU* 1.3 78.5 - - - +
219B PRO* 1.3 71.4 - - + +
221B ALA* 3.3 1.0 + - - +
222B VAL* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.1 13.5 - - + -
79B VAL* 4.0 25.8 - - + -
89B ALA* 4.2 11.0 - - + -
93B ILE* 3.6 23.1 - - + +
114B VAL* 4.7 1.8 - - + +
141B ASN* 3.6 17.9 - - - +
143B ILE* 4.4 3.6 - - + -
214B PRO 4.0 0.2 - - - +
215B VAL 3.6 18.6 - - - +
216B GLY 3.4 9.0 - - - +
218B LEU* 1.3 96.4 - - + +
220B ILE* 1.3 60.6 - - - +
222B VAL* 3.3 2.9 + - - +
223B SER* 3.1 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 4.4 12.1 - - - +
92B ALA* 3.5 28.5 - - + -
93B ILE* 4.2 4.0 - - + -
211B VAL* 4.5 12.1 - - + +
216B GLY* 2.9 34.1 + - - +
217B LEU* 3.8 4.7 - - - +
219B PRO* 1.3 76.6 - - - +
221B ALA* 1.3 61.7 + - - +
223B SER* 2.7 25.5 + - - -
225B LEU* 3.4 26.8 + - + -
227B ILE* 3.8 11.0 - - + -
230B MSE 3.7 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.7 3.8 - - + +
64B GLN* 5.3 2.7 - - + -
67B ALA* 3.7 20.4 - - + +
71B LYS* 3.2 16.3 + - - -
217B LEU 3.0 18.4 + - - +
218B LEU 3.7 2.2 - - - +
220B ILE* 1.3 76.1 - - - +
222B VAL* 1.3 63.7 + - - +
224B GLY* 3.0 12.3 + - - -
225B LEU 3.7 14.5 + - - +
227B ILE* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 3.9 22.0 - - - -
70B ILE* 3.9 25.8 - - + -
71B LYS* 3.7 13.8 - - + +
77B LEU* 3.8 32.3 - - + -
111B THR* 3.7 1.0 - - - -
112B PRO* 3.6 39.5 - - + +
114B VAL* 4.8 4.5 - - + -
218B LEU* 3.0 23.6 + - + +
219B PRO 3.3 5.8 + - - +
221B ALA* 1.3 75.9 - - - +
223B SER* 1.3 59.0 + - - +
224B GLY 3.1 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.8 16.6 - - - +
97B ASN* 3.1 42.0 + - - +
101B TYR* 3.4 18.3 + - - -
111B THR* 3.5 14.4 + - - +
114B VAL* 4.3 6.1 - - - -
219B PRO 3.1 10.8 + - - -
220B ILE 2.7 20.1 + - - -
221B ALA 3.2 0.2 - - - -
222B VAL* 1.3 74.8 - - - +
224B GLY* 1.3 56.0 + - - +
225B LEU* 3.5 7.1 - - - +
----------------------------------------------------------
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