Contacts of the helix formed by residues 174 - 184 (chain B) in PDB entry 4COO
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 SER 174 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B MET* 4.5 0.2 - - - +
173B MET* 1.3 76.7 - - - +
175B SER* 1.3 63.1 + - - +
176B GLU* 3.4 9.0 - - - -
177B LYS* 3.1 38.0 + - - +
178B VAL* 3.5 7.8 + - - +
304B GLU* 3.0 14.3 + - - -
380B ASN 2.7 29.0 + - - -
384B LYS* 3.7 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A MET* 4.2 24.5 - - - -
173B MET 3.8 1.6 + - - -
174B SER* 1.3 70.2 - - - +
176B GLU* 1.3 69.3 + - - +
178B VAL* 3.0 12.6 + - - +
179B ASP* 2.9 38.7 + - - -
383B THR* 4.5 5.2 + - - -
384B LYS* 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MET* 3.7 17.6 - - + +
174B SER* 3.1 16.5 - - - -
175B SER* 1.3 82.9 + - - +
177B LYS* 1.3 63.2 + - - +
179B ASP* 3.5 13.4 + - - +
180B VAL* 3.3 27.5 + - - +
379B ARG 3.4 26.9 - - - +
380B ASN* 3.5 12.0 - - - +
381B TYR* 4.5 0.9 - - - -
382B MET* 3.6 13.0 + - + +
383B THR* 2.5 51.9 + - - +
384B LYS* 4.7 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B SER* 2.9 30.1 + - - +
148B GLY* 4.0 9.9 - - - -
149B ASN* 4.5 7.2 - - - +
152B ILE* 4.2 17.9 - - + +
169B MET* 4.2 11.2 - - + -
173B MET* 4.0 2.7 - - + -
174B SER* 3.1 26.6 + - - +
176B GLU* 1.3 76.1 - - - +
178B VAL* 1.3 64.8 + - - +
180B VAL* 3.4 3.1 + - - +
181B LEU* 3.0 30.7 + - + +
304B GLU* 2.7 41.6 + - - +
305B GLY* 5.5 0.8 - - - -
380B ASN* 3.5 34.3 - - - +
381B TYR* 4.0 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLU* 3.9 9.4 - - + +
505A MET* 4.1 11.2 - - - -
169B MET* 3.7 13.9 - - + -
174B SER 4.0 6.5 - - - +
175B SER* 3.0 10.9 + - - +
177B LYS* 1.3 76.0 - - - +
179B ASP* 1.3 58.1 + - - +
181B LEU* 3.2 8.6 + - - +
182B ARG* 2.8 65.5 + - - +
188B ILE* 3.9 13.2 - - + +
190B ARG* 3.3 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A MET* 3.8 22.4 - - + +
383A THR* 5.5 3.1 - - - +
386A LEU* 3.7 28.8 - - + +
387A SER* 5.7 4.6 - - - -
175B SER* 2.9 23.7 + - - +
176B GLU* 3.5 19.1 - - - +
178B VAL* 1.3 78.1 - - - +
180B VAL* 1.3 59.9 + - - +
182B ARG* 3.6 19.5 + - - +
183B ALA* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.2 16.6 - - + -
378A VAL* 5.0 6.1 - - + -
382A MET* 4.0 13.2 - - + -
386A LEU* 4.4 7.4 - - + -
152B ILE* 4.2 22.0 - - + -
176B GLU 3.3 15.9 + - - +
177B LYS 3.9 3.1 - - - +
179B ASP* 1.3 76.5 - - - +
181B LEU* 1.3 66.1 + - - +
183B ALA* 3.2 6.1 + - - +
184B LEU* 2.9 41.9 + - + +
379B ARG* 3.7 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLY 4.8 2.7 - - - +
151B GLY 3.5 33.0 - - - +
152B ILE* 3.7 16.4 - - + +
155B ALA* 4.0 8.1 - - + -
167B ILE* 3.9 33.4 - - + -
169B MET* 4.1 24.2 - - + -
177B LYS* 3.0 23.5 + - + +
178B VAL* 3.6 4.0 - - - +
180B VAL* 1.3 77.6 - - - +
182B ARG* 1.3 59.3 + - - +
184B LEU* 3.3 6.0 + - - -
185B GLY 3.2 4.2 + - - -
186B ALA* 2.9 29.6 + - + +
188B ILE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASP* 5.6 8.1 - - - -
501A HIS* 3.9 18.4 + - - +
504A GLU* 2.5 46.6 + - - +
505A MET* 4.6 10.3 - - - +
178B VAL* 2.8 39.9 + - - +
179B ASP* 3.8 18.8 + - - +
181B LEU* 1.3 73.3 - - - +
183B ALA* 1.3 59.0 + - - +
185B GLY* 2.8 21.0 + - - -
186B ALA 4.3 8.7 - - - +
188B ILE* 3.7 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ARG* 4.6 5.0 - - + +
339A ILE* 3.6 20.4 - - + +
340A ALA* 3.5 23.9 + - - +
386A LEU* 3.5 34.3 - - + +
179B ASP 3.2 8.6 + - - +
180B VAL* 3.2 6.3 + - - +
182B ARG* 1.3 79.4 - - - +
184B LEU* 1.3 58.9 + - - +
185B GLY 3.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 3.6 31.0 - - + +
340A ALA* 4.5 7.3 - - - +
343A GLY* 4.2 5.2 - - - -
345A LEU* 4.5 4.3 - - + -
152B ILE* 3.8 28.0 - - + +
155B ALA* 4.0 18.0 - - + +
156B LEU* 4.0 35.0 - - + +
159B ALA* 3.7 21.2 - - + +
180B VAL* 2.9 37.9 + - + +
181B LEU* 3.7 5.4 - - - +
182B ARG 3.2 0.2 - - - -
183B ALA* 1.3 75.4 - - - +
185B GLY* 1.3 60.7 + - - +
186B ALA 3.4 0.8 + - - -
----------------------------------------------------------
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