Contacts of the helix formed by residues 112 - 123 (chain F) in PDB entry 2ARP
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 112 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 6.0 1.6 - - + -
98F TRP 5.8 0.2 - - - +
99F LYS* 4.2 12.3 - - - +
100F GLY 3.4 14.1 - - - +
102F VAL* 4.0 7.0 - - - -
110F TYR* 3.1 11.2 - - - +
111F ARG* 1.3 96.8 - - - +
113F GLU* 1.3 62.3 + - - +
114F CYS* 2.9 18.0 + - - +
115F ALA* 2.8 33.1 + - - +
116F LEU 3.4 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 3.3 39.0 - - + +
97F THR 5.3 0.5 + - - -
98F TRP* 4.2 14.9 + - - +
100F GLY 4.2 3.0 + - - -
102F VAL* 4.1 15.6 - - + +
112F ASN* 1.3 73.4 - - - +
114F CYS* 1.4 59.5 + - - +
116F LEU* 3.2 4.8 + - + +
117F LEU* 2.9 42.1 + - + +
129F VAL* 3.9 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F PRO* 5.3 1.6 - - - -
93F CYS* 2.1 54.5 - - + -
96F ILE* 3.5 10.7 - - + +
112F ASN* 2.9 13.8 + - - +
113F GLU* 1.4 76.1 - - - +
115F ALA* 1.3 63.9 + - - +
117F LEU* 3.3 3.7 + - - +
118F LYS* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F TYR* 3.9 17.4 - - + -
111F ARG* 4.5 7.2 - - + +
112F ASN* 2.8 30.7 + - - +
114F CYS* 1.3 72.1 - - - +
116F LEU* 1.3 63.3 + - - +
118F LYS* 3.5 6.6 + - - +
119F ALA* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F VAL* 3.9 15.7 - - + -
104F GLY* 3.6 30.5 - - - -
110F TYR* 3.8 27.5 - - + -
112F ASN 3.4 7.7 + - - +
113F GLU* 3.2 10.4 + - + +
114F CYS 3.2 0.8 - - - -
115F ALA* 1.3 79.2 - - - +
117F LEU* 1.3 69.9 + - + +
119F ALA* 3.3 3.8 + - - +
120F ARG* 2.9 27.6 + - + +
127F LEU* 3.7 24.3 - - + +
128F GLU* 3.7 13.9 - - - +
129F VAL* 3.8 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F PRO* 3.9 19.5 - - + +
92F ASP 4.0 21.1 - - - +
93F CYS* 4.4 9.9 - - - -
96F ILE* 4.8 7.0 - - + -
113F GLU* 2.9 35.6 + - + +
114F CYS* 3.3 5.6 + - - +
116F LEU* 1.3 83.6 - - + +
118F LYS* 1.3 57.9 + - - +
120F ARG* 3.5 24.2 + - - +
121F CYS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F CYS* 4.4 19.3 + - + +
91F PRO* 3.8 17.4 - - + +
114F CYS* 3.1 17.3 + - - +
115F ALA* 3.8 7.9 - - - +
117F LEU* 1.3 74.2 - - - +
119F ALA* 1.3 53.4 + - - +
121F CYS* 3.3 2.6 + - - +
122F LYS* 2.8 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F TYR* 3.9 13.0 - - + -
115F ALA 3.1 14.2 + - - +
116F LEU 3.6 7.4 - - - +
118F LYS* 1.3 72.5 - - - +
120F ARG* 1.3 58.7 + - - +
122F LYS* 4.4 5.4 - - - +
123F GLU* 2.8 49.1 + - - +
124F GLN 3.0 7.8 + - - -
127F LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F LEU* 2.9 17.4 + - - +
117F LEU* 3.6 25.5 - - - +
118F LYS 3.3 0.2 - - - -
119F ALA* 1.3 75.9 - - - +
121F CYS* 1.3 62.8 + - - +
124F GLN 3.2 36.2 + - - +
125F PRO* 3.1 34.2 + - + +
126F GLU* 3.4 19.0 + - - +
127F LEU* 2.8 41.6 + - + +
128F GLU* 3.7 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.6 6.8 + - - -
111A GLU* 5.3 3.6 - - - +
74F GLY* 4.2 10.5 - - - -
75F LYS* 3.9 25.3 + - - -
89F CYS* 2.0 53.1 - - + -
91F PRO* 4.8 7.0 - - + -
117F LEU 3.1 17.2 + - - +
118F LYS* 3.3 4.0 + - - +
120F ARG* 1.3 79.1 - - - +
122F LYS* 1.3 62.2 + - - +
125F PRO* 5.9 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.0 24.7 + - - +
89F CYS* 3.7 15.5 - - + +
118F LYS* 2.8 45.5 + - + +
119F ALA* 4.2 4.0 - - - +
121F CYS* 1.3 79.2 - - - +
123F GLU* 1.3 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.2 26.7 - - - +
88A PRO* 3.3 19.4 - - + +
110F TYR* 4.0 4.2 + - - -
119F ALA* 2.8 37.4 + - - +
121F CYS 3.6 0.2 - - - -
122F LYS* 1.3 79.8 - - + +
124F GLN* 1.3 87.0 + - + +
125F PRO* 3.9 0.2 - - - -
----------------------------------------------------------
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