Contacts of the helix formed by residues 133 - 145 (chain C) in PDB entry 5LPN
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 133 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 4.2 15.5 - - + +
131C VAL 3.8 5.8 - - - +
132C VAL* 1.3 97.4 - - - +
134C LYS* 1.3 68.0 + - - +
135C GLY 3.3 2.7 - - - +
136C LYS* 3.3 40.1 - - + +
137C GLY 4.0 1.2 + - - -
150C GLU* 4.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ARG* 3.9 14.3 - - - +
133C PRO* 1.3 74.8 - - - +
135C GLY* 1.3 57.7 + - - +
137C GLY* 3.9 0.5 + - - -
138C GLU* 2.8 45.0 + - - +
150C GLU* 3.5 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C PRO* 4.2 3.0 - - - +
134C LYS* 1.3 76.5 - - - +
136C LYS* 1.3 66.7 + - - +
137C GLY 3.1 2.0 - - - -
138C GLU* 3.4 15.7 + - - -
139C GLN* 3.0 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PHE* 5.9 5.0 - - + -
131C VAL* 4.3 8.8 + - - +
132C VAL* 3.2 34.6 - - + +
133C PRO* 3.3 49.0 + - + +
135C GLY* 1.3 77.6 - - - +
137C GLY* 1.3 56.4 + - - +
139C GLN* 4.9 0.9 - - - +
140C ILE* 3.5 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 6.1 1.6 - - - -
97C PHE* 4.9 15.7 - - - -
119C LEU* 5.9 1.9 - - - +
132C VAL* 4.6 2.7 - - - +
133C PRO 4.0 2.0 + - - -
134C LYS 3.9 2.8 + - - -
135C GLY 3.1 0.2 - - - -
136C LYS* 1.3 77.8 - - - +
138C GLU* 1.3 60.0 + - - +
139C GLN 3.1 2.9 - - - -
140C ILE* 2.8 30.8 + - - +
141C ALA* 2.9 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C LYS* 2.8 42.7 + - - +
135C GLY* 3.3 10.7 + - - -
137C GLY* 1.3 79.1 - - - +
139C GLN* 1.3 63.8 + - - +
141C ALA* 3.1 13.8 + - + +
142C ARG* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLY* 3.0 32.4 + - - +
136C LYS 4.9 2.0 - - - +
138C GLU* 1.3 85.8 + - - +
140C ILE* 1.3 62.1 + - + +
142C ARG* 3.3 13.6 + - + +
143C GLU* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PHE* 6.1 2.9 - - + -
100C ILE* 6.5 0.9 - - + -
119C LEU* 6.0 7.6 - - + -
136C LYS 3.5 11.2 - - - +
137C GLY* 3.1 27.1 - - - +
139C GLN* 1.3 76.8 - - + +
141C ALA* 1.3 56.8 + - - +
143C GLU* 2.9 51.1 + - + +
144C HIS* 3.1 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 5.6 4.0 - - + +
137C GLY 2.9 8.9 + - - +
138C GLU* 3.1 20.8 + - + +
140C ILE* 1.3 76.5 - - - +
142C ARG* 1.3 57.5 + - - +
144C HIS* 3.2 2.2 + - - -
145C GLY* 2.8 25.8 + - - -
146C ILE* 3.4 41.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C GLU 2.9 12.8 + - - +
139C GLN* 3.7 18.4 - - + +
141C ALA* 1.3 76.3 - - - +
143C GLU* 1.3 62.0 + - - +
144C HIS 3.4 0.3 + - - -
145C GLY* 3.5 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLN* 2.9 25.2 + - - +
140C ILE* 2.9 53.0 + - - +
142C ARG* 1.3 78.5 - - - +
144C HIS* 1.3 68.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU* 5.3 16.0 - - + +
117C ARG* 6.0 4.9 - - - -
140C ILE* 3.1 22.9 + - + +
141C ALA* 3.2 1.1 + - - +
143C GLU* 1.3 87.4 - - + +
145C GLY* 1.3 61.7 + - - +
146C ILE* 3.3 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ALA 2.8 10.2 + - - -
142C ARG* 3.5 11.8 + - - -
144C HIS* 1.3 76.2 - - - +
146C ILE* 1.3 60.6 + - - -
----------------------------------------------------------
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