Contacts of the helix formed by residues 110 - 120 (chain V) in PDB entry 3J0S
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 110 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78V LYS* 2.7 33.0 - - - +
79V ASP* 4.6 6.1 - - - +
80V CYS 5.7 0.7 - - - +
108V SER 3.9 1.1 - - - +
109V ALA* 1.4 76.9 - - + +
111V LEU* 1.3 66.3 + - - +
112V LYS* 3.3 5.5 + - + +
113V SER* 3.5 13.3 + - - +
114V LYS* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K ASP* 4.2 25.4 - - + +
144K ALA 6.1 0.4 - - - +
334K GLU* 4.1 34.5 - - + +
341K ILE* 5.5 4.3 - - + -
107V GLU* 5.9 4.9 - - - +
109V ALA 3.1 7.0 + - - +
110V PRO* 1.3 72.2 - - - +
112V LYS* 1.3 67.5 + - + +
114V LYS* 4.4 10.5 - - + -
115V MET* 2.9 68.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLY 5.3 7.2 - - - +
25K ASP* 3.7 26.9 + - - +
345K ILE* 5.8 1.8 - - + +
44V LYS* 4.4 1.7 - - - -
110V PRO* 3.3 4.0 - - + -
111V LEU* 1.3 89.9 - - + +
113V SER* 1.3 62.0 + - - +
115V MET* 4.0 3.7 + - - +
116V ILE* 3.9 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40V LEU* 5.7 2.1 - - - +
44V LYS* 3.8 29.4 + - - +
80V CYS* 4.5 17.0 + - - +
110V PRO* 3.5 16.9 + - - +
112V LYS* 1.3 77.5 - - - +
114V LYS* 1.3 65.5 + - - +
115V MET 3.5 0.3 + - - -
116V ILE 3.5 2.4 + - - -
117V TYR* 3.3 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K ALA 3.1 25.6 - - - -
145K SER* 3.2 23.1 + - - +
146K GLY* 3.4 13.1 - - - -
80V CYS* 4.0 20.8 - - + +
105V ALA* 3.6 17.0 + - - +
106V PRO 3.2 23.0 + - - +
107V GLU* 4.2 15.0 - - - +
109V ALA* 4.0 10.1 - - + +
110V PRO 3.1 21.3 + - - +
111V LEU* 4.0 9.9 - - + +
113V SER* 1.3 79.7 - - - +
115V MET* 1.3 58.4 + - - +
117V TYR* 3.1 3.9 + - - +
118V ALA* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 115 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144K ALA* 4.5 26.5 - - + +
341K ILE* 3.1 33.4 - - + +
342K GLY* 4.7 4.0 - - - +
345K ILE* 3.4 49.5 - - + +
111V LEU* 2.9 40.8 + - + +
112V LYS* 4.4 3.4 - - - +
113V SER 3.3 0.2 - - - -
114V LYS* 1.3 82.1 - - - +
116V ILE* 1.3 61.7 + - - +
118V ALA* 3.5 6.0 + - + +
119V SER* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 116 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345K ILE* 3.3 31.4 - - + +
346K LEU* 4.9 6.2 - - + +
349K LEU* 3.9 37.0 - - + -
4V GLY* 5.8 1.3 - - - +
5V VAL* 4.8 3.4 - - + -
40V LEU* 3.6 14.8 - - + -
44V LYS* 3.3 43.5 - - + -
112V LYS 3.9 11.8 + - - +
113V SER 3.5 1.4 + - - -
114V LYS 3.3 0.4 - - - -
115V MET* 1.3 75.7 - - - +
117V TYR* 1.3 59.0 + - - +
119V SER* 3.4 4.6 + - - -
120V SER* 2.9 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K GLY 4.9 2.0 - - - -
40V LEU* 4.6 7.8 - - + +
80V CYS* 3.1 30.5 - - + +
81V ARG 2.9 18.8 + - - -
82V TYR* 3.0 69.2 + + - -
103V PHE* 3.2 24.1 - + - -
104V TRP 2.9 38.5 + - - -
105V ALA* 3.4 20.0 - - + -
113V SER* 3.3 10.0 + - - +
114V LYS 3.1 10.0 + - - +
116V ILE* 1.3 79.8 - - - +
118V ALA* 1.3 66.5 + - - +
120V SER* 3.2 5.6 + - - -
121V LYS* 3.5 6.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143K TYR* 2.8 50.3 - - - +
144K ALA* 3.8 4.5 - - - +
146K GLY* 3.3 28.7 - - - +
148K THR* 5.1 0.3 + - - -
114V LYS* 2.9 23.8 + - - +
115V MET* 3.8 5.8 - - - +
117V TYR* 1.3 80.9 - - - +
119V SER* 1.3 53.4 + - - +
120V SER 3.3 0.2 + - - -
121V LYS* 3.5 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143K TYR* 3.1 32.7 + - - -
144K ALA* 5.8 1.2 - - - -
342K GLY* 4.9 1.2 + - - -
345K ILE* 5.5 1.2 - - - +
346K LEU* 3.4 31.7 - - - +
1V MET* 3.4 24.3 - - - +
2V ALA 4.7 1.7 - - - +
4V GLY 3.8 11.6 + - - -
115V MET* 3.1 22.4 + - - +
116V ILE* 3.8 4.3 - - - -
118V ALA* 1.3 76.4 - - - +
120V SER* 1.3 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4V GLY* 4.3 10.1 - - - +
5V VAL* 3.2 36.3 - - - +
40V LEU* 5.0 0.9 - - - -
47V ILE* 4.3 3.6 - - - +
82V TYR* 3.0 23.2 + - - -
116V ILE* 2.9 17.4 + - - -
117V TYR 3.2 0.8 + - - -
119V SER* 1.3 76.0 - - - +
121V LYS* 1.3 57.3 + - - +
122V ASP 3.3 2.9 - - - -
123V ALA* 3.1 4.1 + - - +
124V ILE* 2.7 27.0 + - - +
----------------------------------------------------------
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