Contacts of the helix formed by residues 117 - 123 (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 PRO 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 4.1 3.1 - - - +
113A LEU* 3.3 28.7 - - - +
114A ASP 3.7 8.7 - - - +
115A ASN 4.1 0.2 - - - -
116A ASP* 1.3 83.6 - - - +
118A SER* 1.3 53.1 + - - +
119A PHE 2.6 18.3 + - - -
120A PHE* 3.4 23.7 + - + +
121A CYS* 4.9 0.7 + - - -
142A VAL* 3.7 31.8 - - + +
146A SER* 5.3 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 2.8 21.6 + - - -
117A PRO* 1.3 75.3 - - - +
119A PHE* 1.3 60.8 + - - +
120A PHE 3.6 0.2 - - - -
121A CYS* 3.5 29.3 - - - +
122A ARG* 4.8 0.9 + - - -
146A SER* 5.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 4.8 2.7 - - + -
60A ILE* 3.4 29.2 - - + -
105A VAL* 4.2 18.8 - - + -
112A LEU* 3.7 24.0 - - + -
116A ASP* 3.2 32.5 + - + +
117A PRO 2.6 8.1 + - - +
118A SER* 1.3 70.9 + - - +
120A PHE* 1.3 66.2 + + + +
121A CYS 2.9 10.8 + - - -
122A ARG* 2.9 71.1 + - - +
123A PHE* 3.8 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A CYS* 4.3 5.8 - - - -
36A ILE* 3.8 28.0 - - + -
60A ILE* 4.0 9.4 - - + -
109A PRO* 5.1 3.4 - - + -
112A LEU* 4.2 30.1 - - + -
113A LEU* 3.7 25.1 - - + -
117A PRO* 3.4 18.3 + - + +
119A PHE* 1.3 77.9 - + + +
121A CYS* 1.3 59.5 + - - +
122A ARG 3.1 3.1 - - - -
123A PHE* 3.2 24.9 + + - +
126A VAL* 3.8 22.2 - - + -
139A LEU* 4.1 14.1 - - + -
142A VAL* 5.3 2.2 - - + -
143A LEU* 3.4 25.6 - - + -
146A SER* 5.9 1.3 - - - -
148A ILE* 3.5 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PRO 4.9 0.4 + - - -
118A SER* 3.5 25.1 + - - +
119A PHE 2.9 1.8 + - - -
120A PHE* 1.3 78.6 - - - +
122A ARG* 1.3 60.6 + - - +
123A PHE 3.2 6.2 + - - +
146A SER* 3.8 34.1 - - - -
148A ILE* 4.0 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 4.3 22.5 + - + +
58A THR* 5.8 0.4 - - - -
116A ASP* 5.7 0.4 + - - -
118A SER 4.8 0.8 + - - -
119A PHE* 2.9 53.2 + - - +
121A CYS* 1.3 79.9 - - - +
123A PHE* 1.3 90.5 + - + +
124A THR* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 3.6 32.8 - + - +
33A VAL 3.9 0.7 - - - -
34A CYS* 3.2 40.4 - - + -
58A THR* 3.6 35.7 - - + -
119A PHE* 3.8 22.0 - + - -
120A PHE* 3.2 22.8 + + + +
121A CYS 3.2 3.3 - - - +
122A ARG* 1.3 106.4 - - + +
124A THR* 1.3 63.6 + - - +
125A VAL 4.1 10.8 - - - +
126A VAL* 4.1 6.1 - - + -
148A ILE* 3.5 20.9 - - + +
----------------------------------------------------------
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