Contacts of the strand formed by residues 179 - 187 (chain A) in PDB entry 1FIU
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 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 4.4 2.2 - - - -
109A GLN* 3.9 35.0 - - + +
110A GLN* 3.8 18.2 - - + +
144A THR* 3.2 7.3 - - - -
145A ARG* 2.8 45.7 + - + +
147A LEU* 4.2 11.4 - - + -
169A SER* 4.1 10.1 - - - +
170A LEU* 3.7 31.4 - - + -
178A PRO* 1.3 75.2 - - - +
180A LEU* 1.3 63.6 + - - +
181A HIS* 3.4 0.6 + - - -
286D VAL* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 4.4 18.6 - - + -
108A TYR* 3.9 19.0 - - + +
110A GLN* 2.9 39.3 + - - +
111A TYR* 3.9 19.3 - - + -
139A PRO* 5.3 2.9 - - + -
142A ILE* 3.8 24.2 - - + -
143A VAL 3.6 16.8 - - - +
144A THR* 4.1 7.0 - - + -
179A LEU* 1.3 72.7 - - - +
181A HIS* 1.3 59.0 + - - +
182A ALA 3.6 15.0 - - - +
183A SER* 5.4 2.0 - - - -
205A LEU* 4.6 6.5 - - + -
214A PRO* 3.8 28.4 - - + +
212D ARG* 4.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 4.1 12.3 - + - -
88A ARG* 3.5 18.5 + - - -
92A TRP* 3.4 33.7 - + + -
143A VAL* 2.8 35.4 + - - +
144A THR* 4.3 2.2 - - - +
145A ARG* 4.7 2.0 - - + +
179A LEU* 3.4 2.5 + - - -
180A LEU* 1.3 73.9 - - - +
182A ALA* 1.3 59.8 + - - +
214A PRO* 3.4 5.2 - - - +
215A HIS* 2.9 41.7 + + - -
284A LEU* 2.8 35.7 + - + +
212D ARG* 3.8 16.2 + - - +
286D VAL 4.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 3.3 8.0 - - - -
143A VAL* 3.0 42.1 + - + -
180A LEU* 3.6 10.5 - - - +
181A HIS* 1.3 82.6 - - - +
183A SER* 1.3 59.2 + - - +
184A ILE* 4.0 7.9 - - + -
214A PRO* 4.0 2.7 - - - +
215A HIS* 3.4 22.9 - - + +
217A VAL* 5.9 0.2 - - + -
284A LEU* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO* 3.3 29.7 - - - +
141A ILE 3.8 3.6 - - - -
142A ILE* 4.9 0.2 - - - -
180A LEU* 5.4 2.5 - - - -
182A ALA* 1.3 71.4 - - - +
184A ILE* 1.3 62.1 + - - +
185A SER* 4.0 4.2 + - - -
205A LEU* 3.6 29.4 - - - +
214A PRO* 4.4 2.0 - - - +
215A HIS 2.8 11.8 + - - +
216A ILE* 4.5 6.1 - - - +
217A VAL* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A CYS* 5.7 0.7 - - + -
77A VAL* 4.3 23.3 - - + -
140A ASP* 3.5 5.0 - - - +
141A ILE* 2.9 66.1 + - + +
143A VAL* 4.0 25.8 - - + -
182A ALA* 4.4 8.3 - - + -
183A SER* 1.3 77.4 + - - +
185A SER* 1.3 62.3 + - - +
186A CYS* 4.5 2.5 - - - -
217A VAL* 3.7 18.8 - - + -
219A VAL* 4.0 27.4 - - + -
280A LEU* 4.5 4.3 - - + -
284A LEU* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO* 6.3 0.9 - - - -
140A ASP* 3.6 8.7 - - - +
183A SER* 4.0 4.8 - - - -
184A ILE* 1.3 74.3 - - - +
186A CYS* 1.3 53.8 + - - +
187A LYS* 4.2 1.4 - - - -
198A ALA* 4.8 1.3 - - - -
201A GLU* 5.8 0.2 - - - -
217A VAL 2.9 14.0 + - - -
218A VAL* 3.1 20.0 - - - +
219A VAL* 2.7 32.4 + - - +
2001A ACY 2.6 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.9 15.9 - - + -
70A GLU* 4.0 21.4 - - + +
73A CYS* 3.9 20.9 - - - -
140A ASP* 2.8 13.1 + - - +
141A ILE* 3.6 32.5 - - - -
184A ILE* 4.4 5.6 - - - -
185A SER* 1.3 77.7 - - - +
187A LYS* 1.3 66.2 + - - +
188A TRP 4.2 0.7 - - - -
219A VAL* 3.3 6.3 - - - -
5555A MG 2.2 30.7 - - - -
6J C 4.2 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.9 2.5 - - - -
185A SER* 4.2 3.1 - - - +
186A CYS* 1.3 80.3 - - - +
188A TRP* 1.3 62.9 + - - +
189A THR 3.2 13.0 - - - +
190A ILE* 4.2 14.6 - - + -
194A ARG* 3.9 9.9 + - - +
195A ALA* 3.6 28.0 - - + +
197A ASN* 2.8 29.3 + - - -
198A ALA* 4.0 12.6 - - - -
218A VAL* 4.5 11.2 - - + -
219A VAL 2.9 8.0 + - - +
220A THR* 2.8 41.4 + - - +
231A ILE* 5.5 2.0 - - + -
2001A ACY 3.0 18.2 + - - +
5555A MG 4.3 0.4 - - - -
5J C 3.6 10.7 + - - -
6J C 3.6 10.5 + - - +
----------------------------------------------------------
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