Contacts of the strand formed by residues 118 - 123 (chain E) in PDB entry 1R5I
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 ASN 118 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E VAL* 1.3 72.3 - - - +
119E VAL* 1.3 62.4 + - - +
120E THR* 3.7 16.4 + - - -
164E ARG 3.4 3.3 + - - +
165E VAL* 3.6 0.7 - - - -
166E GLU* 3.0 68.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ILE* 3.3 29.4 - - + -
117E VAL* 4.0 12.1 + - + -
118E ASN* 1.3 79.5 + - - +
120E THR* 1.3 74.4 + - - +
121E TRP* 5.0 3.4 - - + +
149E HIS* 3.3 46.6 + - + +
163E CYS* 3.7 28.3 - - - -
164E ARG 3.3 4.0 - - - +
165E VAL* 4.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASN* 3.7 15.9 + - - -
119E VAL* 1.3 83.9 + - - +
121E TRP* 1.3 74.0 + - - +
122E LEU* 3.8 9.3 + - + +
127E PRO* 4.3 13.0 - - + -
128E VAL 6.0 0.2 - - - +
162E ASP 3.7 1.6 - - - +
163E CYS* 3.7 0.6 - - - -
164E ARG* 2.9 74.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E VAL* 4.6 8.3 - - + -
105E LEU* 3.6 44.2 - - + -
106E ILE 4.3 1.6 - - - -
107E CYS* 3.7 30.7 - - + -
119E VAL* 5.4 1.3 - - + -
120E THR* 1.3 76.8 - - - +
122E LEU* 1.3 60.1 + - - +
127E PRO* 3.2 8.1 - - - +
128E VAL* 2.9 37.9 + - + +
132E VAL* 3.6 25.1 - - + +
149E HIS* 3.7 33.7 - + + +
150E TYR 3.6 14.5 + - - -
151E LEU* 3.5 29.6 - - + -
161E TYR* 5.0 3.1 - - + -
162E ASP 3.8 13.7 - - - -
163E CYS* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E THR* 4.2 10.5 - - + +
121E TRP* 1.3 76.8 - - - +
123E ARG* 1.3 60.3 + - - +
124E ASN 4.0 0.4 - - - -
125E GLY* 3.9 18.8 - - - +
126E LYS 3.4 3.6 - - - -
127E PRO* 3.5 38.4 - - + -
128E VAL* 4.5 0.7 - - - -
161E TYR* 3.1 11.4 - - - +
162E ASP* 3.0 45.4 + - - +
164E ARG* 3.5 42.6 - - + +
175E LEU* 4.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E LEU* 1.3 71.8 - - - +
124E ASN* 1.3 70.8 + - - +
125E GLY 3.2 0.2 - - - -
126E LYS* 2.9 67.5 + - - +
128E VAL* 3.4 48.3 - - + +
130E THR* 5.9 0.6 + - - -
151E LEU* 5.4 2.0 - - - +
152E PRO 5.8 0.4 + - - -
153E PHE* 5.4 4.0 - - - +
159E ASP* 3.9 27.1 - - + +
160E VAL 3.7 3.4 - - - +
161E TYR* 3.3 41.1 + - + -
----------------------------------------------------------
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