Contacts of the strand formed by residues 150 - 156 (chain A) in PDB entry 1R4N
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 LEU 150 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 5.4 0.2 - - - -
126A VAL* 3.4 18.2 - - + +
128A ALA* 4.3 9.4 - - + -
139A LEU* 3.7 15.7 - - + -
140A ALA* 3.3 45.1 - - + +
143A LEU* 3.2 29.8 - - + -
148A ILE 3.5 2.9 + - - +
149A PRO* 1.3 76.1 - - - +
151A LEU* 1.3 63.9 + - - +
152A ILE* 3.8 21.1 - - + -
164A ILE* 3.6 4.7 - - - +
165A ILE* 2.8 50.1 + - + +
508A ILE* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.9 5.2 - - + -
126A VAL 2.9 13.4 + - - +
127A VAL* 3.4 13.5 - - + +
128A ALA 2.9 25.8 + - - +
150A LEU* 1.3 74.9 - - - +
152A ILE* 1.3 60.5 + - - +
153A CYS* 3.6 18.9 + - - -
162A MET* 4.1 14.8 - - + -
163A ARG 3.4 18.8 - - - +
164A ILE* 3.7 23.8 - - + -
501A ALA* 3.9 17.3 - - + +
504A GLU* 4.4 8.5 - - + -
505A VAL* 3.7 26.2 - - + -
508A ILE* 5.5 4.3 - - + -
516A PHE* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 3.3 15.5 - - + +
131A LEU* 5.2 7.9 - - + +
136A SER* 4.0 26.5 - - - +
140A ALA* 4.5 1.1 - - + -
150A LEU* 3.8 33.0 - - + -
151A LEU* 1.3 68.9 - - - +
153A CYS* 1.3 68.0 + - - +
154A ARG* 5.4 2.5 - - + -
161A TYR* 4.5 17.9 - - + +
162A MET* 3.3 3.1 - - - +
163A ARG* 2.8 47.7 + - + +
165A ILE* 4.4 5.8 - - + -
398A LEU* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 4.4 7.6 - - + -
45A ILE* 3.7 21.8 - - + -
127A VAL* 4.4 2.0 - - - -
128A ALA 2.7 8.8 + - - +
129A THR* 3.2 9.8 - - + -
130A GLN* 3.1 21.4 + - - -
131A LEU 5.0 0.2 + - - -
151A LEU* 3.8 22.0 - - - -
152A ILE* 1.3 83.7 - - - +
154A ARG* 1.3 63.5 + - - +
161A TYR 3.5 6.1 - - - +
162A MET* 3.8 9.9 - - - -
497A LEU* 4.6 4.0 - - + -
501A ALA* 3.7 29.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 5.1 0.7 - - - -
130A GLN* 3.1 19.4 - - - +
131A LEU 4.2 19.6 + - - +
152A ILE* 5.4 2.7 - - + -
153A CYS* 1.3 78.1 - - - +
155A THR* 1.3 65.8 + - - +
156A TYR* 4.1 22.2 + - + +
159A VAL 3.8 1.0 - - - +
160A GLY* 3.7 0.2 - - - -
161A TYR* 2.7 64.8 + - + +
429A LEU* 4.3 26.6 + - + +
432A VAL* 4.7 4.0 - - - +
433A ASP* 2.7 43.0 + - - -
442A TYR* 3.6 25.7 + - - -
497A LEU* 3.1 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 2.7 26.9 + - - -
130A GLN* 2.5 33.8 + - - +
154A ARG* 1.3 73.0 - - - +
156A TYR* 1.3 69.1 + - - +
157A GLY 4.3 0.2 - - - +
159A VAL 3.7 3.1 - - - -
487A ALA 5.3 1.2 - - - +
488A ALA 4.4 3.3 - - - +
489A GLU* 3.9 29.2 - - + +
490A PRO* 4.1 4.0 - - + -
493A ILE* 3.4 29.2 - - + +
494A ALA* 3.5 13.8 + - - +
497A LEU* 3.5 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ARG* 4.1 21.7 - - + +
155A THR* 1.3 77.8 - - - +
157A GLY* 1.3 58.7 + - - +
158A LEU 3.0 0.2 + - - -
159A VAL* 2.7 43.0 + - + +
429A LEU* 4.0 19.1 - - + -
432A VAL* 3.3 24.5 - - + +
442A TYR* 3.5 20.4 - + - +
443A PRO* 3.4 16.3 + - - +
482A PHE* 3.7 49.6 + + - -
485A TYR* 4.0 6.7 - + + -
487A ALA* 3.3 37.7 + - + -
488A ALA 3.9 1.3 - - - -
----------------------------------------------------------
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