Contacts of the helix formed by residues 180 - 196 (chain B) in PDB entry 6FF8
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 ASN 180 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.4 16.4 - - + -
172B GLU* 2.9 32.8 + - - +
173B THR* 4.3 3.7 - - + +
178B ASN 4.0 2.0 + - - -
179B ILE* 1.3 82.3 - - - +
181B ILE* 1.3 57.6 + - - +
182B GLU 3.4 1.6 - - - -
183B GLU* 3.3 27.9 + - + +
184B ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.1 27.1 - - + +
44B ARG* 4.1 11.7 - - + -
45B TYR* 3.6 36.3 - - + +
141B LEU* 6.0 0.7 - - + -
173B THR* 4.1 13.5 - - + -
174B SER 3.3 28.0 - - - +
175B ALA* 3.5 21.8 - - + +
178B ASN* 4.2 10.9 + - - +
179B ILE 3.0 9.1 + - - +
180B ASN* 1.3 75.1 - - - +
182B GLU* 1.3 58.7 + - - +
184B ALA* 3.3 6.0 + - - +
185B ALA* 2.9 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 3.3 35.8 + - - +
48B GLN* 3.9 18.1 + - - -
65B LYS* 4.5 5.5 + - - -
178B ASN* 4.9 14.7 - - - +
180B ASN 3.4 0.2 - - - -
181B ILE* 1.3 77.9 - - + +
183B GLU* 1.3 66.5 + - - +
185B ALA* 3.5 2.9 + - - +
186B ARG* 3.0 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PHE* 4.1 16.3 - - + -
180B ASN* 3.3 36.9 + - + +
182B GLU* 1.3 80.3 + - - +
184B ALA* 1.3 61.7 + - - +
186B ARG* 3.3 6.6 + - - +
187B PHE* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.8 9.7 - - + -
139B VAL* 4.8 0.2 - - - +
141B LEU* 3.7 31.2 - - + -
171B PHE* 3.8 23.1 - - + -
173B THR* 4.8 1.3 - - + -
180B ASN 2.9 19.9 + - - +
181B ILE* 3.6 5.8 - - - +
183B GLU* 1.3 76.1 - - - +
185B ALA* 1.3 62.6 + - - +
187B PHE* 3.3 4.0 + - - +
188B LEU* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 3.1 46.0 - - + +
67B LEU* 5.0 0.7 - - + -
77B LEU* 5.3 3.4 - - + -
103B PHE* 3.9 18.2 - - + -
181B ILE* 2.9 15.3 + - + +
182B GLU 3.7 2.9 - - - +
184B ALA* 1.3 76.9 - - - +
186B ARG* 1.3 60.0 + - - +
188B LEU* 3.4 2.8 + - - +
189B VAL* 3.0 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 5.6 0.7 - - - +
67B LEU* 4.4 11.6 - - + +
68B ASN 3.9 10.9 + - - -
69B TRP* 3.0 80.0 + - + +
70B ASP* 5.4 0.2 - - - +
182B GLU* 3.0 22.2 + - + +
183B GLU* 3.3 7.4 + - - +
185B ALA* 1.3 75.8 - - + +
187B PHE* 1.3 57.9 + - - +
189B VAL* 3.3 1.9 + - - -
190B GLU* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.8 18.2 - - + -
168B ALA* 3.5 35.0 - - + -
169B GLY* 4.0 9.9 - - - -
171B PHE* 3.5 28.0 - + + -
183B GLU 2.9 16.6 + - - +
184B ALA 3.5 3.4 - - - +
186B ARG* 1.3 73.6 - - - +
188B LEU* 1.3 65.3 + - - +
190B GLU* 3.4 16.0 - - - +
191B LYS* 3.2 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.9 20.0 - - + -
101B GLY* 4.4 1.8 - - - -
102B ALA 3.7 19.5 - - - +
103B PHE* 3.7 29.4 - - + -
137B PRO* 3.8 36.8 - - + +
139B VAL* 3.7 25.4 - - + -
184B ALA 3.1 16.4 + - - +
185B ALA 3.4 3.6 + - - +
186B ARG 3.3 0.2 - - - -
187B PHE* 1.3 77.0 - - - +
189B VAL* 1.3 58.8 + - + +
191B LYS* 3.2 4.4 + - + +
192B ILE* 2.9 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.8 3.6 - - + -
28B VAL* 6.3 0.2 - - + -
67B LEU* 4.0 20.4 - - + -
69B TRP* 3.6 25.4 - - + -
75B VAL* 4.1 19.3 - - + -
77B LEU* 4.2 24.5 - - + -
185B ALA 3.0 18.2 + - - +
186B ARG 3.7 3.8 - - - +
188B LEU* 1.3 73.4 - - + +
190B GLU* 1.3 60.8 + - - +
192B ILE* 3.2 9.9 + - + +
193B LEU* 2.8 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TRP* 3.7 29.1 - - + -
186B ARG 2.8 13.7 + - - +
187B PHE* 3.4 20.3 - - - +
189B VAL* 1.3 77.6 - - - +
191B LYS* 1.3 75.5 + - - +
193B LEU* 3.3 4.1 + - - +
194B VAL* 3.1 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PRO* 3.9 19.3 - - + -
168B ALA* 3.9 27.1 - - + -
187B PHE* 3.2 51.7 + - + +
188B LEU* 3.2 10.2 + - + +
190B GLU* 1.3 93.1 + - - +
192B ILE* 1.3 63.2 + - - +
194B VAL* 3.3 27.7 - - + +
195B ASN* 3.3 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.8 30.1 - - + -
28B VAL* 4.0 22.0 - - + -
77B LEU* 5.3 2.0 - - + -
100B VAL* 3.8 39.3 - - + +
101B GLY* 4.0 20.9 - - - +
137B PRO* 4.2 8.5 - - + -
188B LEU* 2.9 28.7 + - + +
189B VAL* 3.2 10.5 + - + +
191B LYS* 1.3 76.2 - - - +
193B LEU* 1.3 58.4 + - - +
195B ASN* 3.3 8.0 + - - +
196B HIS* 2.9 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 6.0 0.7 - - - +
24B HIS* 3.8 34.5 - - + +
26B PHE* 3.9 17.0 - - + -
69B TRP* 3.7 42.8 - - + +
73B THR* 4.6 5.8 - - + -
75B VAL* 4.7 1.8 - - + -
189B VAL* 2.8 33.7 + - + +
190B GLU* 3.7 4.5 - - - +
192B ILE* 1.3 75.2 - - - +
194B VAL* 1.3 66.2 + - + +
196B HIS* 3.2 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU* 3.1 22.2 + - + +
191B LYS* 3.3 23.8 - - + +
193B LEU* 1.3 78.0 - - + +
195B ASN* 1.3 71.9 + - - +
196B HIS 3.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 3.6 25.8 - - + +
132B ASN* 5.8 2.1 + - - -
135B PRO 5.1 0.8 + - - -
137B PRO* 3.4 32.9 - - - +
191B LYS* 3.4 13.5 + - - +
192B ILE* 3.3 9.4 + - + +
194B VAL* 1.3 86.3 - - - +
196B HIS* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ARG* 5.8 7.4 - - - +
24B HIS* 3.8 19.4 - + + +
26B PHE* 3.5 30.3 - + + -
192B ILE* 2.9 18.2 + - + +
193B LEU* 3.2 17.9 + - + +
194B VAL 4.4 2.9 - - - -
195B ASN* 1.3 82.7 - - - +
----------------------------------------------------------
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