Contacts of the strand formed by residues 137 - 143 (chain E) 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 ASP 137 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D LYS* 5.4 0.2 - - - -
164D TYR 5.0 2.1 + - - -
167D GLY* 3.6 12.3 - - - -
168D ASN* 2.7 35.9 + - - +
135E PHE* 3.6 3.8 - - - +
136E ASP* 1.3 85.7 - - + +
138E ILE* 1.3 61.4 + - - +
139E ARG* 2.6 36.0 + - - +
150E ALA 4.6 1.4 - - - +
151E ILE* 3.7 1.6 - - - -
152E ASP* 2.9 48.6 + - + +
252E THR* 4.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D SER 4.0 1.7 - - - +
168D ASN* 3.0 31.6 + - - +
170D GLY* 3.9 15.6 - - - +
135E PHE* 5.0 3.1 - - + -
137E ASP* 1.3 75.5 - - - +
139E ARG* 1.3 66.9 + - - +
140E PHE* 4.0 13.8 - - + -
149E VAL* 4.3 9.6 - - + -
150E ALA 3.4 15.9 - - - +
151E ILE* 4.0 21.8 - - + -
252E THR* 4.0 5.4 - - + +
462K PHE* 4.4 7.9 - - + -
466K TYR* 3.6 53.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D SER 3.3 8.7 - - - +
161D SER* 3.6 15.0 + - - +
162D THR 3.5 19.7 - - - +
163D LYS* 3.5 42.0 - - - +
168D ASN* 3.8 6.7 - - + +
137E ASP* 2.6 43.4 + - - +
138E ILE* 1.3 80.0 - - - +
140E PHE* 1.3 65.0 + - - +
148E HIS* 4.4 7.7 + - - +
149E VAL* 3.2 2.1 - - - +
150E ALA* 2.6 61.0 + - + +
152E ASP* 5.8 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D SER* 3.0 56.8 + - - -
161D SER* 3.3 2.4 + - - -
170D GLY* 4.9 13.2 - - - -
138E ILE* 4.0 22.0 - - + -
139E ARG* 1.3 81.0 - - - +
141E GLY* 1.3 64.0 + - - +
148E HIS* 3.0 28.3 + - - +
149E VAL* 3.9 5.6 - - + -
459K PRO 4.5 3.6 - - - +
462K PHE* 3.6 37.7 - - + -
463K GLU* 3.4 35.9 - - + -
466K TYR* 4.5 11.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D SER* 4.5 4.9 - - - -
161D SER* 4.8 2.9 - - - -
140E PHE* 1.3 82.6 - - - +
142E ALA* 1.3 59.9 + - - -
147E SER* 3.0 5.3 - - - -
148E HIS* 2.8 44.5 + - - +
459K PRO* 4.4 4.1 + - - +
463K GLU* 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E GLY* 1.3 75.2 - - - +
143E SER* 1.3 61.5 + - - +
146E GLY 3.5 6.1 - - - +
147E SER* 3.8 13.0 - - - -
452E ARG* 4.6 6.9 + - - +
456E THR* 4.8 6.1 - - + +
460K VAL* 4.1 19.1 - - + +
463K GLU* 4.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E ALA* 1.3 77.5 - - - +
144E ILE* 1.3 68.7 + - - +
145E SER* 3.0 22.7 + - - -
146E GLY* 2.7 20.1 + - - +
158K TRP* 6.1 0.3 - - - +
261K PHE* 5.5 8.0 - - - +
----------------------------------------------------------
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