Contacts of the helix formed by residues 108 - 116 (chain C) 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 SER 108 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 4.4 1.3 - - - -
62C GLY* 3.8 14.7 - - - +
107C GLU* 1.3 78.2 - - - +
109C PRO* 1.3 75.2 - - - +
110C GLU* 3.9 6.1 + - - +
111C ASN* 3.0 27.3 + - - +
112C LEU* 3.2 21.8 + - - +
274H ARG* 4.3 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.5 41.3 - - + -
37C ASN* 4.4 13.2 - - - +
60C ILE* 4.6 9.6 - - + +
62C GLY 5.2 0.7 - - - +
107C GLU 4.7 0.4 - - - +
108C SER* 1.3 86.5 - - - +
110C GLU* 1.3 70.1 + - + +
112C LEU* 2.8 9.2 + - + +
113C LEU* 2.8 32.0 + - + +
120C PHE* 5.3 2.5 - - + -
131C LEU* 4.6 7.9 - - + -
135C THR* 4.2 17.3 - - + -
139C LEU* 6.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C SER* 4.2 6.3 - - - +
109C PRO* 1.3 83.4 - - + +
111C ASN* 1.3 54.9 + - - +
112C LEU 2.8 10.7 + - - -
113C LEU* 3.0 13.2 + - - +
114C ASP* 3.0 22.3 + - - +
134C SER* 3.9 8.3 + - - +
135C THR* 2.4 47.2 + - + +
138C ARG* 2.9 35.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU* 2.8 39.5 + - - +
108C SER* 3.0 28.1 + - - +
109C PRO 3.2 0.2 - - - -
110C GLU* 1.3 77.5 - - - +
112C LEU* 1.3 62.1 + - - +
114C ASP* 4.0 5.2 - - - -
115C ASN* 3.0 35.1 + - - +
344G ASN* 4.8 12.8 - - - +
348G GLU* 3.5 18.4 + - - +
274H ARG* 4.9 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.7 42.2 - - + -
105C VAL* 4.6 13.5 - - + -
107C GLU* 4.9 5.4 - - + +
108C SER 3.2 10.7 + - - +
109C PRO* 2.8 8.3 + - + +
110C GLU 2.8 0.6 + - - -
111C ASN* 1.3 87.3 - - - +
113C LEU* 1.3 55.0 + - - +
114C ASP 2.6 14.9 + - - -
115C ASN* 6.0 1.1 - - + -
116C ASP* 2.8 46.6 + - + +
117C PRO* 4.8 0.2 - - - -
119C PHE* 3.7 23.3 - - + -
120C PHE* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PRO* 2.8 23.2 + - + +
110C GLU* 3.7 5.6 - - - +
112C LEU* 1.3 71.3 - - - +
114C ASP* 1.3 53.0 + - - +
117C PRO* 3.3 20.1 - - + +
120C PHE* 3.7 24.0 - - + -
135C THR* 4.4 12.6 - - + +
138C ARG* 2.7 45.7 + - + +
139C LEU* 3.6 48.0 - - + +
142C VAL* 3.8 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLU* 3.0 20.4 + - - +
111C ASN* 4.0 6.6 + - - +
112C LEU 2.6 1.4 + - - -
113C LEU* 1.3 80.9 - - - +
115C ASN* 1.3 72.8 + - - +
116C ASP 3.3 2.5 + - - -
117C PRO* 3.7 7.3 - - - +
138C ARG* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASN* 3.0 33.1 + - - +
112C LEU* 3.3 2.7 + - + -
114C ASP* 1.3 85.9 - - - +
116C ASP* 1.3 65.2 + - + +
117C PRO* 4.1 0.4 - - - -
348G GLU* 3.5 42.8 + - - +
352G LYS* 5.0 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LEU* 2.8 29.4 + - + +
115C ASN* 1.3 79.0 - - + +
117C PRO* 1.3 67.1 - - - +
118C SER* 2.8 27.0 + - - -
119C PHE* 3.2 33.6 + - + +
120C PHE* 5.0 0.2 - - - -
122C ARG* 5.7 0.7 + - - -
----------------------------------------------------------
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