Contacts of the strand formed by residues 176 - 185 (chain L) in PDB entry 6AHR
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 LYS 176 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L ASN* 3.8 44.5 - - + +
72L LEU 3.4 11.7 - - - +
73L PRO* 4.4 4.7 - - + -
174L PRO 4.0 3.1 + - - +
175L LEU* 1.3 73.8 - - - +
177L PHE* 1.3 78.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LYS* 3.8 24.7 - - - -
71L ASN* 3.3 4.6 + - - +
72L LEU 2.9 29.1 + - - -
74L LEU* 4.7 2.2 - - + -
96L THR* 3.7 22.2 - - + -
99L THR* 4.2 16.2 - - + -
105L ASN* 3.6 42.4 - - + -
107L VAL* 4.2 15.7 - - + -
175L LEU* 4.0 31.0 - - + -
176L LYS* 1.3 87.9 - - - +
178L ASP* 1.3 64.6 + - - +
179L PHE* 3.3 27.3 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LYS 5.3 2.8 - - - +
68J SER* 5.3 4.7 + - - -
68L PHE* 3.7 29.6 - - + -
69L VAL 3.3 3.6 - - - -
70L LYS* 3.4 10.5 - - - +
71L ASN* 3.1 27.9 + - - +
96L THR* 3.3 2.9 - - - -
97L TYR* 2.7 53.7 + - + +
99L THR* 6.3 0.2 - - - +
177L PHE* 1.3 72.0 - - - +
179L PHE* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L TYR 3.6 0.5 - - - +
68L PHE* 3.4 7.8 - - - -
69L VAL* 2.9 36.7 + - + +
72L LEU* 3.3 46.4 - - + -
73L PRO 5.1 0.4 - - - -
74L LEU* 3.6 28.5 - - + -
77L LEU* 4.2 15.7 - - + -
94L ALA* 4.6 9.6 - - + -
95L LEU 3.4 20.0 - - - -
96L THR* 3.7 25.8 - - + -
107L VAL* 4.4 9.0 - - + -
177L PHE* 3.3 31.4 - - + -
178L ASP* 1.3 70.7 - - - +
180L LEU* 1.3 60.2 + - - +
181L LEU* 4.0 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H VAL* 5.3 11.2 - - + -
66L TYR* 3.8 26.2 - - + -
67L TYR 3.3 8.7 - - - +
68L PHE* 3.6 25.4 - - + -
93L TYR 3.8 0.3 - - - +
94L ALA* 3.2 6.6 - - - -
95L LEU* 2.8 38.2 + - + +
96L THR 5.4 3.4 - - - +
97L TYR* 4.6 21.5 - - + -
178L ASP 4.1 0.4 + - - -
179L PHE* 1.3 72.8 - - - +
181L LEU* 1.3 59.7 - - - +
284L PHE* 4.2 33.7 - - + -
317L PHE* 4.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L TYR* 3.6 5.0 - - - +
67L TYR* 2.9 37.8 + - + +
69L VAL* 3.7 28.9 - - + -
72L LEU* 4.7 7.0 - - + -
77L LEU* 5.2 6.3 - - + -
82L PHE* 5.4 1.6 - - + -
92L CYS* 5.3 7.4 - - - -
93L TYR 3.3 5.2 - - - +
94L ALA* 3.7 26.9 - - + -
179L PHE* 4.4 16.2 - - + +
180L LEU* 1.3 76.1 - - - +
182L ALA* 1.3 63.1 + - - +
193L MET* 3.7 21.1 - - + -
197L PHE* 3.8 30.7 - - + -
202L ILE* 5.1 0.2 - - + -
284L PHE* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L PRO 4.7 11.2 - - - +
66L TYR* 5.2 0.4 - - - +
67L TYR* 5.0 4.7 - - - -
91L SER 4.4 0.7 - - - -
92L CYS* 3.5 5.7 - - - -
93L TYR* 2.9 32.4 + - + +
181L LEU* 1.3 77.9 - - - +
183L TRP* 1.3 64.4 + - - +
184L HIS 4.3 0.2 - - - -
193L MET* 4.1 6.4 - - - +
284L PHE* 3.6 26.0 - - + -
286L LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 183 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L TYR* 5.8 1.8 - - - -
85L THR 3.6 18.2 - - - -
86L PHE* 2.6 52.1 + + + -
89L LYS* 3.3 24.0 - - + -
90L GLY* 3.4 9.7 - - - -
91L SER 3.3 19.7 - - - -
92L CYS* 3.9 4.9 - - - -
182L ALA* 1.3 78.2 - - - +
184L HIS* 1.3 62.7 + - - +
185L LYS* 3.4 47.1 + - + +
186L THR 5.4 0.2 - - - -
187L GLY* 5.7 2.5 - - - -
189L GLU 4.7 12.3 - - - -
190L GLU* 5.5 1.3 - - - -
191L SER* 3.6 29.8 - - - -
192L THR* 5.9 0.7 - - - -
193L MET* 3.7 18.3 - - + +
286L LEU* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 184 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L GLY* 3.3 4.2 - - - -
91L SER* 2.9 49.1 + - - +
93L TYR* 5.8 0.7 - - + -
183L TRP* 1.3 71.3 + - - +
185L LYS* 1.3 74.5 + - - +
186L THR* 3.5 15.5 + - + -
286L LEU* 4.7 22.7 - - + +
288L GLU* 3.8 47.1 + - + +
289L LYS* 6.0 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 185 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L TRP* 3.7 44.6 - - + +
184L HIS* 1.3 79.0 + - - +
186L THR* 1.3 65.7 + - - +
187L GLY 3.7 7.2 - - - +
190L GLU* 5.2 24.2 + - + +
191L SER 5.6 3.1 - - - +
192L THR* 5.9 6.8 - - - +
----------------------------------------------------------
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