Contacts of the strand formed by residues 123 - 128 (chain F) in PDB entry 3PRJ
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 TYR 123 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F PHE* 3.7 43.9 - + + -
82F ALA 4.9 0.9 - - - +
83F ASP* 4.7 4.3 - - - +
121F ASN 3.9 1.2 + - - +
122F GLY* 1.3 71.9 - - - -
124F LYS* 1.3 70.5 + - - +
125F ILE* 3.8 22.4 - - + +
153F ASN* 3.1 38.4 - - + +
155F GLN* 3.7 27.4 - - + +
187F GLU* 4.2 14.5 + - - -
190F ARG* 4.6 11.5 - - - -
191F ALA* 3.7 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ILE 3.0 12.9 + - - +
80F LYS 2.7 28.4 + - - -
81F GLU 4.0 1.0 - - - -
82F ALA 2.7 34.8 + - - +
83F ASP 3.6 6.1 - - - +
85F VAL* 4.8 10.3 - - + -
116F ILE* 5.6 0.9 - - + -
120F SER* 3.1 37.9 - - - +
121F ASN 3.9 15.1 + - - +
122F GLY 3.9 1.0 + - - +
123F TYR* 1.3 84.9 + - - +
125F ILE* 1.3 66.4 + - - +
126F VAL* 4.0 2.0 - - + -
152F LEU* 6.4 0.2 - - + -
153F ASN 3.2 9.6 + - - +
154F LEU* 3.5 18.3 - - + -
155F GLN* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F PHE* 4.2 9.4 - - + -
4F ILE* 4.4 8.1 - - + -
83F ASP 2.9 12.1 + - - +
84F LEU* 3.3 22.0 - - + +
85F VAL* 2.7 32.6 + - - +
123F TYR* 3.8 33.0 - - + +
124F LYS* 1.3 76.0 - - - +
126F VAL* 1.3 58.1 + - - +
127F THR* 3.8 2.5 - - - +
155F GLN* 3.6 6.1 - - + +
157F LEU* 3.8 29.2 - - + -
191F ALA* 4.0 13.0 - - + +
194F ALA* 3.9 28.0 - - + -
195F LEU* 5.5 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F VAL* 3.4 14.4 - - + +
87F ILE* 3.8 29.4 - - + -
116F ILE* 4.2 13.9 - - + -
124F LYS* 5.0 1.8 - - + -
125F ILE* 1.3 75.4 - - - +
127F THR* 1.3 56.5 + - - +
140F ILE* 4.5 7.6 - - + -
144F PHE* 3.5 38.1 - - + -
154F LEU* 4.1 17.5 - - + -
155F GLN 2.7 16.5 + - - +
156F VAL* 3.4 4.2 - - - +
157F LEU 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F LEU* 3.4 21.2 - - - +
85F VAL 2.9 9.3 + - - -
86F PHE* 3.3 32.6 - - + -
87F ILE 2.8 25.6 + - - -
125F ILE* 3.8 0.7 + - - +
126F VAL* 1.3 76.2 - - - +
128F GLU* 1.3 64.6 + - - +
129F LYS 3.7 0.7 + - - -
157F LEU* 3.3 25.5 - - + +
159F ASN* 3.5 31.6 - - + +
195F LEU* 4.0 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ILE* 3.8 11.0 - - + +
89F VAL 5.4 0.2 - - - +
109F ILE* 3.5 23.1 - - + +
126F VAL 4.2 0.2 - - - -
127F THR* 1.3 72.5 - - - +
129F LYS* 1.3 59.6 + - - +
130F SER* 2.9 35.8 + - - -
133F PRO* 3.6 14.6 - - - +
136F ALA* 3.6 25.3 - - + +
137F ALA* 5.1 4.9 - - - +
140F ILE* 3.8 25.0 - - + +
157F LEU 2.9 15.5 + - - +
158F SER* 3.8 5.1 + - - +
159F ASN 2.9 26.2 + - - -
160F PRO* 4.3 1.0 - - - +
217F GLU* 4.1 2.6 - - - +
----------------------------------------------------------
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