Contacts of the strand formed by residues 148 - 155 (chain A) in PDB entry 1PR1
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 ALA 148 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.3 17.5 - - + +
105A ILE* 3.6 29.8 - - + -
138A VAL* 5.2 8.5 - - + +
141A ALA* 4.1 18.6 - - + -
146A ILE 3.7 2.4 + - - -
147A ASP* 1.3 75.6 + - - +
149A ARG* 1.3 63.6 + - - +
150A VAL* 3.8 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A HIS* 2.7 36.0 + - - +
98A VAL* 3.8 24.8 - - - +
99A LYS* 5.1 1.2 - - - +
102A ASP* 2.9 28.0 + - + -
103A VAL 2.9 12.5 + - - +
104A VAL* 3.4 14.8 - - + -
105A ILE* 2.7 34.0 + - - +
147A ASP 5.4 2.2 - - - +
148A ALA* 1.3 74.5 - - - +
150A VAL* 1.3 54.6 + - - +
176A LEU* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.3 15.0 - - + +
107A MET* 3.8 31.5 - - + +
134A VAL* 3.9 15.9 - - + -
138A VAL* 3.5 32.5 - - + -
148A ALA 3.8 6.5 + - - +
149A ARG* 1.3 78.7 - - - +
151A GLY* 1.3 59.3 + - - +
176A LEU* 3.5 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE 3.0 7.5 + - - -
106A GLY* 3.4 6.8 - - - -
107A MET* 2.9 29.2 + - - -
108A GLY 3.4 3.9 + - - -
150A VAL* 1.3 77.2 - - - +
152A ASN* 1.3 62.0 + - - -
174A GLY 5.8 0.2 - - - -
176A LEU* 3.1 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY* 3.1 27.2 - - - -
109A ALA 3.4 2.8 + - - -
110A CYS* 3.7 26.2 - - - -
151A GLY* 1.3 73.7 - - - -
153A LEU* 1.3 61.4 + - - +
173A TYR 5.3 5.3 + - - +
174A GLY 4.8 4.4 + - - +
175A ILE* 3.5 16.1 - - + +
176A LEU* 2.8 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A CYS* 5.0 0.9 - - - -
104A VAL* 4.0 24.9 - - + +
106A GLY* 3.8 24.7 - - - +
108A GLY 2.9 11.1 + - - +
109A ALA* 4.1 5.4 - - + -
110A CYS* 2.7 34.5 + - - +
152A ASN* 1.3 75.8 - - - +
154A PHE* 1.3 55.4 + - - +
175A ILE* 4.6 2.7 - - - -
177A GLY* 3.5 23.8 - - - +
179A GLU* 4.2 20.4 - - + +
182A ALA* 3.7 15.0 - - + -
186A TYR* 5.1 0.4 - - - +
198A THR* 3.0 28.7 - - - +
200A CYS* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A CYS* 3.4 20.0 - - + -
111A THR* 4.0 15.9 - - - -
112A ASP* 3.8 29.4 - - + -
153A LEU* 1.3 74.1 - - - +
155A SER* 1.3 59.4 + - - +
156A ALA* 3.6 32.5 - - + -
166A MET* 4.2 23.6 - - + -
170A MET* 3.6 39.3 - - + -
175A ILE* 3.9 22.9 - - + +
177A GLY 3.1 7.5 + - - +
178A VAL* 4.3 4.9 - - + -
179A GLU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 4.3 5.5 - - - +
109A ALA* 4.1 1.6 - - - +
110A CYS 2.7 14.9 + - - -
111A THR* 2.8 31.6 + - - -
112A ASP* 3.4 4.3 + - - +
154A PHE* 1.3 72.4 - - - +
156A ALA* 1.3 62.6 + - - +
179A GLU* 2.5 26.0 + - - -
180A MET 4.1 2.9 - - - -
181A GLU 4.1 9.9 - - - -
182A ALA* 3.4 1.9 + - - +
183A ALA* 3.0 35.7 + - - +
----------------------------------------------------------
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