Contacts of the strand formed by residues 171 - 182 (chain B) in PDB entry 1F5J
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 171 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ASN* 3.4 25.4 - - - +
54B GLN* 3.3 33.7 - - - +
55B ASN* 3.6 14.5 + - - +
84B SER* 3.0 3.0 - - - -
85B THR* 2.8 49.9 + - - +
86B ASN* 4.2 6.6 + - - +
170B GLY* 1.3 69.4 - - - -
172B ILE* 1.3 63.4 + - - +
173B ASP* 3.4 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 3.3 11.6 - - + -
53B ASN* 3.0 31.0 + - - -
54B GLN 3.1 9.4 + - - +
56B TRP* 3.4 39.0 - - + +
59B LEU* 3.9 9.2 - - + -
83B TRP 3.7 2.9 - - - +
84B SER* 4.1 6.3 - - - -
91B PHE* 4.2 6.7 - - + -
159B PHE* 4.1 6.7 - - + -
169B LEU* 3.8 25.1 - - + -
170B GLY 3.8 7.4 - - - +
171B THR* 1.3 71.0 - - - +
173B ASP* 1.3 61.6 + - - +
174B GLN 3.9 10.3 - - - +
175B ILE* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS* 3.2 23.1 + - - +
52B TYR 2.9 28.5 + - - +
53B ASN* 5.1 1.3 - - - +
83B TRP* 2.8 14.7 + - + +
85B THR* 4.9 5.3 - - + +
131B ILE* 3.8 28.8 - - + +
171B THR* 3.4 4.1 + - - +
172B ILE* 1.3 73.9 - - - +
174B GLN* 1.3 89.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 4.0 10.3 + - + -
47B ARG* 3.0 38.6 + - - +
50B LYS 3.2 12.6 - - - +
51B LYS* 3.3 21.9 - - + +
52B TYR* 4.3 2.0 - - - -
81B TYR* 4.6 0.9 - - - -
82B GLY* 3.2 21.6 - - - -
83B TRP* 3.3 24.0 + - + +
91B PHE* 3.6 3.5 - - - -
131B ILE* 3.7 17.0 - - - +
172B ILE* 3.7 1.7 - - - +
173B ASP* 1.3 102.2 + - - +
175B ILE* 1.3 68.2 + - - +
176B THR* 3.9 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS 2.9 29.5 + - - -
52B TYR* 3.6 24.7 - - + +
59B LEU* 4.5 1.6 - - + -
62B ILE* 4.0 22.0 - - + -
64B ILE* 3.8 24.0 - - + -
80B ILE* 4.0 13.9 - - + -
81B TYR 3.7 2.5 - - - -
82B GLY* 4.5 0.9 - - - -
91B PHE* 4.3 7.9 - - + -
155B VAL* 4.2 13.7 - - + -
159B PHE* 4.2 19.5 - - + -
172B ILE* 3.8 16.2 - - + -
174B GLN* 1.3 79.6 - - - +
176B THR* 1.3 64.2 + - - +
195B PHE* 3.4 10.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 4.7 7.2 - - + -
47B ARG* 3.3 30.9 - - + +
48B THR 3.3 13.5 - - - +
49B GLY* 3.9 14.8 - - - +
50B LYS 4.6 1.3 - - - +
64B ILE* 4.9 3.6 - - - -
80B ILE* 3.1 12.6 - - - +
81B TYR* 2.7 54.8 + - - +
174B GLN* 3.9 22.2 - - + +
175B ILE* 1.3 84.3 - - - +
177B LEU* 1.3 57.8 + - - +
195B PHE* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.7 6.1 - - + -
47B ARG* 3.3 3.8 - - - -
48B THR* 2.9 26.3 + - - +
64B ILE* 5.2 0.2 - - + -
66B TYR* 3.5 44.0 - - + -
67B SER 5.1 0.4 - - - +
78B LEU* 4.5 13.2 - - + -
79B CYS* 3.5 15.9 - - - +
80B ILE* 4.0 17.5 - - + -
95B GLU* 6.3 0.9 - - + -
176B THR* 1.3 71.4 - - - +
178B CYS* 1.3 58.3 + - - +
190B ILE* 3.5 39.7 - - + -
192B GLN 3.7 1.3 - - - +
193B ASN* 3.5 27.9 + - - +
195B PHE* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 4.8 0.2 - - - -
45B LEU* 3.9 30.5 - - - -
46B PHE 3.3 10.1 - - - -
47B ARG* 3.6 15.3 - - + -
78B LEU* 3.5 5.6 - - - +
79B CYS* 2.6 47.7 + - - +
81B TYR* 3.6 27.6 - - + -
176B THR* 4.1 0.2 - - - +
177B LEU* 1.3 76.0 - - - +
179B VAL* 1.3 78.7 + - - +
180B GLU* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 4.2 3.1 - - + -
36B CYS* 3.9 15.3 - - - -
38B TRP* 3.6 37.2 - - + -
45B LEU* 3.4 1.4 - - - -
46B PHE* 2.8 40.8 + - + +
70B TYR* 4.2 5.2 - - + -
76B SER* 4.4 0.2 - - - +
77B TYR 3.4 8.1 - - - +
78B LEU* 4.0 11.7 - - + -
178B CYS* 1.3 77.6 - - - +
180B GLU* 1.3 61.6 + - - +
188B ALA* 3.9 14.4 - - + -
190B ILE* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 5.0 0.2 - - - -
43B ASN* 3.1 24.4 + - - +
44B ALA 3.3 11.0 - - - +
45B LEU* 3.5 24.1 - - + +
46B PHE* 5.9 0.2 - - - -
76B SER* 2.6 29.5 + - - -
77B TYR* 2.9 44.1 + - + +
79B CYS* 5.4 0.4 - - - -
92B TYR* 2.6 40.6 + - + -
178B CYS* 4.1 4.4 - - - -
179B VAL* 1.3 77.7 - - - +
181B GLY* 1.3 60.8 + - - +
182B TYR* 5.6 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 3.8 23.5 - - - -
41B ILE* 3.3 8.5 - - - +
43B ASN* 2.9 21.8 + - - -
44B ALA* 2.8 20.4 + - - +
46B PHE* 5.7 0.8 - - - -
75B ASN 3.7 7.9 - - - -
76B SER* 5.0 0.4 - - - -
180B GLU* 1.3 75.9 - - - +
182B TYR* 1.3 59.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.7 0.2 - - - +
42B ASN* 3.1 35.0 + - - -
43B ASN* 4.0 18.4 - - + +
75B ASN* 3.0 55.0 + - + +
77B TYR* 6.1 2.2 - - + +
180B GLU* 5.6 2.5 - - + +
181B GLY* 1.3 73.3 - - - +
183B GLN* 1.3 106.9 + - + +
184B SER* 3.2 4.1 + - - -
----------------------------------------------------------
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