Contacts of the helix formed by residues 159 - 169 (chain B) in PDB entry 6N0M
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 LEU 159 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.6 35.0 - - + -
118B MET* 4.0 9.2 - - + -
155B LYS 4.0 0.8 + - - +
156B LEU* 3.2 19.0 + - + +
157B ARG 3.0 0.2 - - - -
158B LYS* 1.3 78.3 - - - +
160B SER* 1.3 56.4 + - - +
161B GLU 3.3 0.4 - - - -
162B ILE* 3.5 15.2 - - + +
163B ASN* 2.8 30.9 + - - +
181B LEU* 3.7 21.8 - - + -
189B TRP* 3.5 33.9 - - + -
194B LEU* 4.4 4.7 - - + -
197B ALA* 4.3 13.9 - - + -
198B LEU* 5.4 0.2 - - + -
201B LEU* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 4.1 6.5 - - - +
122B ARG* 4.9 2.4 + - - -
149B LEU* 3.2 24.8 - - - +
157B ARG 3.1 11.8 + - - -
158B LYS 3.2 0.2 - - - -
159B LEU* 1.3 77.0 - - - +
161B GLU* 1.3 57.9 + - - +
163B ASN* 3.5 6.9 + - - +
164B LYS* 2.9 30.5 + - - +
316B VAL* 5.3 0.3 - - - -
317B GLU* 3.1 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS 4.1 7.0 + - - +
159B LEU 3.3 0.6 - - - -
160B SER* 1.3 78.7 - - - +
162B ILE* 1.3 62.5 + - - +
164B LYS* 3.1 35.8 + - - +
165B LEU* 3.0 40.7 + - + +
177B HIS* 3.5 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS 4.7 1.0 + - - +
159B LEU* 3.5 25.8 - - + +
161B GLU* 1.3 76.9 - - - +
163B ASN* 1.3 67.2 + - - +
165B LEU* 4.5 7.0 - - - +
166B LEU* 3.0 38.5 + - + +
173B ILE* 4.2 25.1 - - + -
177B HIS* 5.2 8.3 - - + -
178B ILE* 3.9 17.0 - - + -
181B LEU* 3.8 34.1 - - + -
198B LEU* 3.8 26.7 - - + -
201B LEU* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 2.8 46.6 + - + +
119B ALA* 3.5 1.1 - - - +
122B ARG* 3.4 12.1 - - - +
159B LEU 2.8 20.1 + - - +
160B SER* 3.5 7.2 + - - +
162B ILE* 1.3 76.1 - - - +
164B LYS* 1.3 66.2 + - - +
166B LEU* 4.5 1.3 - - - -
167B ALA* 3.2 19.2 + - - +
201B LEU* 3.6 23.6 - - + +
205B HIS* 2.8 35.7 + - - -
315B PHE 5.2 1.8 + - - -
316B VAL* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.4 37.0 - - - +
160B SER 2.9 17.3 + - - +
161B GLU* 3.4 34.0 + - - +
163B ASN* 1.3 79.0 - - - +
165B LEU* 1.3 66.3 + - - +
168B HIS* 3.0 34.7 + - - +
317B GLU 4.1 1.8 - - - +
318B ASP* 3.2 34.9 + - + +
321B PHE* 3.6 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU* 3.0 24.4 + - - +
162B ILE* 4.3 2.0 - - - +
164B LYS* 1.3 91.9 - - - +
166B LEU* 1.3 64.7 + - - +
169B ARG 2.8 42.4 + - - +
170B PRO* 2.9 11.1 - - - -
172B LEU* 4.1 12.6 - - + -
173B ILE* 3.8 24.2 - - + +
177B HIS* 3.5 40.2 - - + +
321B PHE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.0 40.6 + - + +
163B ASN 3.7 4.3 - - - +
165B LEU* 1.3 75.6 - - - +
167B ALA* 1.3 63.6 + - - +
170B PRO* 3.7 5.4 - - - +
173B ILE* 3.5 19.9 - - + +
198B LEU* 4.5 9.9 - - + +
201B LEU* 4.0 28.3 - - + -
202B THR* 3.7 20.6 - - + -
205B HIS* 3.9 13.6 + - + +
463B ARG* 4.4 2.3 + - - -
467B ALA* 3.5 47.7 - - + +
471B ALA* 3.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 4.1 5.2 - - + -
123B HIS* 3.9 7.0 - - - +
163B ASN 3.2 6.5 + - - +
164B LYS 3.5 7.9 - - - +
165B LEU 3.1 0.6 - - - -
166B LEU* 1.3 81.2 - - - +
168B HIS* 1.3 82.8 + - + +
170B PRO* 4.5 0.3 - - - +
205B HIS* 3.5 21.9 - - + +
401B PHE* 4.3 9.7 - - - -
429B ALA 5.0 0.5 - - - +
430B CYS* 6.0 0.3 - - - -
463B ARG* 2.6 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.2 56.7 + - - +
123B HIS* 3.7 22.6 - + - -
164B LYS 3.0 22.4 + - - +
167B ALA* 1.3 82.8 - - + +
169B ARG* 1.3 65.5 + - - +
170B PRO* 3.6 5.9 - - - +
321B PHE* 3.6 40.2 + + + -
322B GLY* 3.8 16.3 - - - -
323B TYR* 3.6 29.4 + - - +
401B PHE* 4.4 1.4 - - - -
430B CYS* 4.6 7.1 + - - +
431B TYR* 6.4 0.4 - + - -
433B GLU* 5.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 2.8 19.8 + - + +
168B HIS* 1.3 82.4 - - - +
170B PRO* 1.3 63.7 - - - +
171B TRP* 3.2 21.1 - - + +
172B LEU* 3.1 41.3 + - + +
321B PHE* 3.3 44.2 - - + +
322B GLY 2.8 26.5 + - - +
323B TYR 3.6 5.0 + - - +
324B GLU 4.0 1.8 + - - -
325B ASP* 3.6 39.4 + - - +
332B GLN* 3.5 25.0 - - - +
----------------------------------------------------------
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