Contacts of the strand formed by residues 28 - 34 (chain L) in PDB entry 1FPY
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 GLU 28 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G PRO* 4.0 0.3 - - - +
182G VAL* 3.3 48.4 + - + +
20L ARG* 3.4 22.8 + - + -
21L PHE 3.5 8.7 - - - +
22L THR* 4.3 0.7 - - - +
26L GLY 3.4 3.8 + - - -
27L LYS* 1.3 73.2 - - - +
29L GLN* 1.3 75.7 + - - +
88L ARG* 2.6 36.9 + - - +
236L GLN* 3.6 38.0 - - - +
237L ILE* 5.1 2.1 + - - +
240L TYR* 4.1 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G TYR 3.0 24.8 - - - +
180G PHE* 3.0 17.6 - - + +
181G PRO* 3.4 6.4 - - - +
182G VAL* 4.3 0.7 - - - -
20L ARG* 3.0 8.8 - - - +
21L PHE* 2.6 73.5 + - + +
23L ASP* 4.1 14.2 + - + +
27L LYS* 2.6 44.3 + - - +
28L GLU* 1.3 88.5 + - - +
30L HIS* 1.3 63.4 + - - +
54L ILE* 5.0 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G PHE* 3.1 33.0 + - - +
181G PRO 3.3 22.8 + - - -
182G VAL* 3.7 8.4 - - + -
183G PRO* 3.5 13.0 - - + -
186G ASP* 3.0 25.8 + - - -
189G GLN* 3.3 27.0 + - + +
192G ARG* 3.7 3.9 + - - -
210G HIS* 4.9 2.1 - - - +
211G HIS* 5.8 2.2 + - + -
18L ASP* 2.9 42.4 - - - +
19L LEU 2.9 8.7 - - - +
20L ARG* 3.6 10.3 - - + -
21L PHE* 5.2 0.7 - - - -
29L GLN* 1.3 79.2 - - - +
31L VAL* 1.3 66.9 + - - +
32L THR* 3.9 1.3 - - - -
80L PHE* 5.1 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G PHE* 4.1 19.5 - - + -
208G ALA* 5.2 2.2 - - + -
209G HIS 3.8 11.9 - - - +
210G HIS* 3.9 17.0 - - + +
17L VAL 3.5 1.0 - - - +
18L ASP* 3.3 1.0 - - - +
19L LEU* 2.7 69.8 + - + +
21L PHE* 5.5 1.3 - - + -
30L HIS* 1.3 79.1 - - - +
32L THR* 1.3 71.7 + - - +
33L ILE* 4.5 8.7 - - + -
67L LEU* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLN* 2.5 32.2 + - - +
192G ARG* 4.3 0.2 + - - -
208G ALA* 3.2 1.0 - - - +
209G HIS* 2.9 64.3 + - + +
16L PHE* 3.6 28.5 - - + -
17L VAL 3.3 12.1 - - - +
18L ASP* 2.7 12.8 + - + +
30L HIS* 3.9 0.9 - - - -
31L VAL* 1.3 72.6 - - - +
33L ILE* 1.3 74.3 - - - +
84L THR* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G GLU 3.4 12.3 - - - +
208G ALA* 3.1 27.4 - - + -
16L PHE* 3.4 4.8 - - - -
17L VAL* 2.6 46.2 + - + +
19L LEU* 4.6 21.1 - - + -
31L VAL* 4.5 10.8 - - + -
32L THR* 1.3 79.7 - - - +
34L PRO* 1.3 73.2 - - - +
37L GLN* 3.6 15.3 - - + +
38L VAL* 4.0 18.4 - - + -
42L PHE* 5.5 4.0 - - + -
47L LYS* 5.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196G CYS* 6.0 0.2 - - - -
200G GLU* 4.7 2.7 - - - +
206G VAL* 3.1 35.9 - - + +
207G GLU 3.1 21.5 - - - +
208G ALA* 3.9 2.7 - - - +
15L LYS 3.7 8.5 - - - +
16L PHE* 3.9 15.9 - - + -
32L THR 4.4 0.2 - - - +
33L ILE* 1.3 95.8 - - - +
35L ALA* 1.3 66.3 + - - +
36L HIS* 3.5 26.5 - - + +
37L GLN* 2.9 17.0 + - + -
----------------------------------------------------------
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