Contacts of the strand formed by residues 171 - 177 (chain A) in PDB entry 1FPD
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 4.7 2.0 - - + -
45A SER* 2.7 26.5 + - - +
49A ARG* 3.3 16.4 + - - +
166A LEU 3.2 4.5 - - - +
167A TYR* 3.7 28.6 - - + -
170A ALA* 1.3 74.1 - - - +
172A MET* 1.3 67.0 + - - +
185A MET* 3.8 5.3 - - - +
186A LEU* 2.9 52.9 + - + +
193A PHE* 4.3 11.7 - - + -
49B ARG 5.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A TYR* 3.9 0.7 - - - +
165A ALA* 3.0 5.9 - - - +
166A LEU* 2.8 38.6 + - + +
170A ALA 3.9 0.4 + - - -
171A THR* 1.3 78.7 - - - +
173A LEU* 1.3 70.5 + - - +
174A VAL* 4.0 7.2 - - + -
183A CYS* 3.9 17.0 - - + -
184A PHE 3.4 13.2 - - - +
185A MET* 4.0 20.0 - - + -
193A PHE* 4.8 0.2 - - - -
196A VAL* 3.4 32.8 - - + -
253A HIS* 3.7 29.2 - - + +
129B LEU* 3.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.1 33.7 - - + -
37A LEU* 5.7 1.8 - - + -
38A CYS* 5.2 4.7 - - - +
41A VAL* 4.1 34.8 - - + -
136A PHE* 4.8 12.8 - - + -
164A TYR 3.5 6.1 - - - +
165A ALA* 4.3 5.6 - - + -
172A MET* 1.3 73.6 - - - +
174A VAL* 1.3 65.3 + - - +
175A LEU* 4.3 21.8 - - + -
183A CYS* 3.6 1.6 - - - -
184A PHE* 2.8 43.7 + - + +
193A PHE* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 4.5 1.6 - - - -
163A GLY* 3.2 5.1 - - - -
164A TYR* 2.9 71.6 + - + +
172A MET* 4.0 8.3 - - + -
173A LEU* 1.3 80.0 - - - +
175A LEU* 1.3 62.9 + - - +
176A ALA 4.2 0.2 - - - -
181A VAL* 3.6 28.3 - - + -
182A ASN 3.5 5.6 - - - +
183A CYS* 4.0 9.2 - - - -
253A HIS* 3.9 17.7 - - + +
256A LEU* 4.1 12.3 - - + -
287A VAL* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 4.5 16.8 - - + -
16A PHE* 4.5 18.4 - - + -
17A VAL* 4.7 9.6 - - + -
34A LEU* 4.4 19.3 - - + -
136A PHE* 4.1 27.8 - - + -
161A ALA* 4.8 2.9 - - + -
162A ALA 4.0 3.1 - - - +
173A LEU* 4.0 12.8 - - + -
174A VAL* 1.3 77.2 - - - +
176A ALA* 1.3 66.2 + - - +
177A MET* 4.2 26.0 - - + -
180A GLY 3.7 2.3 - - - +
181A VAL* 3.5 2.1 - - - +
182A ASN* 3.0 36.5 + - + +
184A PHE* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 3.4 1.6 - - - +
162A ALA 2.8 42.1 + - - +
174A VAL 4.2 0.2 - - - -
175A LEU* 1.3 74.8 - - - +
177A MET* 1.3 65.9 + - - +
180A GLY 3.5 4.7 - - - -
181A VAL* 4.0 11.9 - - + +
286A TYR* 3.5 24.2 - - + -
287A VAL* 3.7 24.9 - - + -
290A LYS* 4.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 5.4 7.9 - - - -
20A GLN* 5.7 1.6 - - - -
30A MET* 3.5 32.3 - - + -
34A LEU* 3.6 20.9 - - + -
160A VAL* 4.1 6.5 - - + +
161A ALA* 3.8 11.2 - - + -
175A LEU* 4.2 21.3 - - + -
176A ALA* 1.3 79.7 - - - +
178A VAL* 1.3 69.3 + - + +
179A ASN* 3.1 20.6 - - - +
180A GLY 2.9 19.1 + - - +
286A TYR* 3.3 11.4 - - - -
290A LYS* 3.5 10.2 - - - +
339A AMP 3.7 31.2 - - + +
----------------------------------------------------------
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