Contacts of the strand formed by residues 184 - 191 (chain C) in PDB entry 1XFB
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 VAL 184 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.2 39.7 - - + +
19C ILE* 3.6 21.1 - - + -
20C ALA* 3.9 11.4 - - + +
23C ILE* 5.2 0.2 - - + -
144C ASP 2.8 12.9 + - - +
145C PHE* 2.9 16.4 - - + +
146C ALA 2.8 25.1 + - - -
183C ILE* 1.3 70.7 - - - +
185C PRO* 1.3 67.4 - - + +
186C ILE* 5.8 0.4 - - + -
226C GLY 3.3 21.8 - - - +
227C THR* 3.9 11.4 - - - -
228C LEU* 4.6 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ALA 4.4 1.1 - - - +
174C TYR* 3.5 24.9 - - + +
175C ALA* 3.8 35.9 - - + +
178C CYS* 3.8 9.4 - - + -
179C GLN* 3.8 8.5 - - + -
183C ILE 3.2 8.3 - - - +
184C VAL* 1.3 86.2 - - - +
186C ILE* 1.3 62.9 + - - +
187C VAL* 3.6 2.9 + - + +
226C GLY 3.2 17.0 - - - +
227C THR* 3.6 12.9 - - + -
228C LEU 3.2 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE* 3.8 20.9 - - + -
78C ILE* 4.1 14.4 - - + -
145C PHE* 3.6 36.1 - - + -
146C ALA 2.8 18.2 + - - +
147C LYS* 4.3 5.8 - - + -
148C TRP 3.7 7.6 + - - -
174C TYR* 2.9 17.6 + - - -
184C VAL* 5.1 0.7 - - + +
185C PRO* 1.3 72.1 - - - +
187C VAL* 1.3 62.3 + - - +
188C GLU* 3.4 4.5 + - + +
228C LEU* 3.4 25.8 - - + +
230C LYS* 3.4 38.1 - - + +
269C THR* 4.5 4.5 - - - +
301C SER* 4.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 3.5 37.7 - - + -
174C TYR* 4.4 7.6 - - + -
175C ALA* 4.5 20.2 - - + -
185C PRO 4.3 7.0 - - - +
186C ILE* 1.3 71.8 - - - +
188C GLU* 1.3 57.2 + - - +
189C PRO* 3.1 9.1 - - + +
213C VAL* 3.9 18.4 - - + -
214C TYR* 5.7 1.6 - - - +
217C LEU* 4.4 19.5 - - + -
227C THR* 4.8 7.4 - - - -
228C LEU 2.8 16.1 + - - +
229C LEU* 3.4 8.0 - - + +
230C LYS 3.0 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LYS* 2.8 36.7 + - + +
148C TRP 3.3 14.2 + - - +
149C ARG* 3.3 31.8 - - + +
150C CYS* 3.0 24.6 + - - +
171C LEU* 4.0 5.1 - - - +
186C ILE* 3.4 7.2 + - + +
187C VAL* 1.3 73.1 - - - +
189C PRO* 1.3 58.2 - - - +
190C GLU* 3.3 14.2 + - - +
230C LYS* 3.3 39.3 - - + +
271C LEU* 3.7 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C CYS* 4.2 6.7 - - + +
152C LEU* 5.6 5.2 - - + -
171C LEU* 3.8 17.7 - - + -
187C VAL* 3.1 17.7 - - + +
188C GLU* 1.3 82.9 - - - +
190C GLU* 1.3 61.7 + - - +
191C ILE* 3.4 8.5 + - - +
209C VAL* 4.2 12.2 - - + +
210C LEU* 4.0 27.1 - - + -
213C VAL* 4.1 13.7 - - + -
229C LEU* 3.8 9.9 - - + -
230C LYS 3.8 6.7 - - - +
231C PRO* 4.5 5.3 - - + +
232C ASN* 3.6 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ARG* 2.4 32.5 + - + +
150C CYS 3.2 16.4 + - - +
151C VAL* 3.4 3.3 - - - +
152C LEU* 2.8 26.6 + - - +
188C GLU* 3.3 17.7 + - + +
189C PRO* 1.3 72.2 - - - +
191C ILE* 1.3 70.1 + - - +
192C LEU* 3.2 23.8 + - + +
193C PRO* 4.7 5.0 - - - +
232C ASN* 4.0 2.9 - - + +
271C LEU* 3.7 40.2 - - + +
273C GLY* 5.0 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU* 3.6 22.4 - - + +
154C ILE* 3.5 37.9 - - + -
189C PRO 4.2 5.2 - - - +
190C GLU* 1.3 75.4 - - - +
192C LEU* 1.3 64.9 + - - +
193C PRO* 3.7 2.9 - - - +
202C CYS* 5.2 4.9 - - - -
205C VAL* 3.7 4.0 - - + -
206C THR* 3.4 42.6 - - + +
209C VAL* 3.6 25.4 - - + -
232C ASN* 2.7 36.9 - - - +
----------------------------------------------------------
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