Contacts of the strand formed by residues 127 - 132 (chain X) in PDB entry 3FEW
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 127 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125X PRO* 4.1 8.7 - - - +
126X ARG* 1.3 82.4 - - + +
128X ILE* 1.3 66.8 + - - +
129X ASP* 4.2 1.7 + - - -
138X ARG* 3.5 46.1 + - + +
139X VAL 3.4 3.6 - - - -
140X THR* 4.3 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125X PRO* 4.0 32.8 - - + +
126X ARG 4.6 0.4 - - - +
127X GLU* 1.3 78.8 - - - +
129X ASP* 1.3 75.3 + - - +
130X VAL* 3.7 11.9 + - + +
137X TYR 3.7 0.9 - - - +
138X ARG* 3.5 1.1 - - - -
139X VAL* 2.8 42.1 + - - +
141X LEU* 3.8 26.7 - - + -
201X ALA* 3.9 14.8 - - + +
204X ALA* 4.0 27.8 - - + -
205X TRP* 5.0 5.2 - - - +
208X LEU* 5.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 129 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127X GLU 4.2 1.9 + - - -
128X ILE* 1.3 77.2 - - - +
130X VAL* 1.3 65.2 + - - +
137X TYR 3.4 4.7 - - - +
138X ARG* 3.5 46.4 + - - +
153X THR* 5.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128X ILE* 4.1 15.0 - - + +
129X ASP* 1.3 80.4 - - - +
131X SER* 1.3 63.5 + - - +
132X ILE* 4.6 4.9 - - + -
136X LYS* 3.7 3.8 - - - +
137X TYR* 2.9 39.0 + - + +
139X VAL* 4.4 3.6 - - + -
197X ALA* 3.6 38.6 - - + +
200X GLN* 3.6 25.1 - - - +
201X ALA* 4.0 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130X VAL* 1.3 77.6 - - - +
132X ILE* 1.3 70.0 + - - +
133X ASP 4.3 0.4 + - - -
134X GLY* 4.4 11.8 + - - -
135X PHE 3.2 10.3 + - - -
136X LYS* 4.1 25.8 + - - -
200X GLN* 4.1 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130X VAL* 4.6 1.8 - - + -
131X SER* 1.3 77.0 + - - +
133X ASP* 1.3 80.2 + - - +
134X GLY 3.1 0.7 - - - -
135X PHE* 2.8 39.7 + - - +
137X TYR* 4.2 11.7 - - + -
193X ARG* 3.8 27.2 - - + +
196X LYS* 4.0 28.5 - - + +
197X ALA* 3.9 28.9 - - + +
200X GLN* 3.5 25.8 - - - +
----------------------------------------------------------
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