Contacts of the helix formed by residues 149 - 159 (chain A) in PDB entry 3LJK
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 ASP 149 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 4.4 5.5 + - - +
144A GLY 3.4 15.6 - - - +
145A ILE* 3.9 7.4 - - - -
146A GLY 3.0 6.2 + - - +
147A GLY 3.4 2.2 + - - -
148A SER* 1.4 76.4 - - - +
150A LEU* 1.3 83.7 + - - +
151A GLY 3.4 2.4 + - - -
152A PRO* 3.5 5.9 - - - +
153A LYS* 3.0 39.7 + - - +
171A PHE* 3.7 25.3 - - - +
172A VAL 4.6 1.0 - - - +
173A SER* 3.7 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY* 2.9 23.4 + - - +
149A ASP* 1.3 88.5 - - - +
151A GLY* 1.3 59.7 + - - +
153A LYS* 3.9 18.2 - - - +
154A MSE 2.9 32.6 + - - +
335A TYR* 5.4 0.3 - - - +
338A ASP* 3.7 34.5 - - + +
339A TYR* 3.8 14.5 - - + +
342A GLN* 3.4 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY 4.7 0.4 + - - -
147A GLY* 5.0 2.8 + - - -
150A LEU* 1.3 79.4 - - - +
152A PRO* 1.3 71.1 - - - +
154A MSE 3.7 0.7 - - - +
155A VAL* 3.0 28.4 + - - +
264A LEU* 3.8 15.0 - - - -
339A TYR* 3.2 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 5.2 1.6 - - - +
147A GLY 4.6 7.6 - - - +
148A SER 5.0 2.2 - - - +
149A ASP* 3.5 17.7 - - - +
151A GLY* 1.3 88.6 - - - +
153A LYS* 1.3 56.3 + - - +
155A VAL* 3.8 0.5 - - - +
156A VAL* 2.9 36.2 + - - +
171A PHE* 3.8 10.1 - - + -
264A LEU* 4.2 9.0 - - + -
268A ILE* 3.8 28.0 - - + +
269A GLY* 4.4 6.7 - - - -
271A SER* 3.3 23.1 - - - +
272A ILE* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASP* 3.0 40.1 + - - +
150A LEU* 3.9 15.9 - - - +
152A PRO* 1.3 75.3 - - - +
154A MSE 1.3 63.7 + - - +
156A VAL* 3.5 1.6 + - - +
157A ARG* 3.1 23.7 + - - +
171A PHE* 3.7 36.8 - - + -
335A TYR* 3.7 46.3 + - + +
338A ASP* 5.1 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU 2.9 19.1 + - - +
151A GLY 3.7 1.1 - - - +
153A LYS* 1.3 77.4 - - - +
155A VAL* 1.3 71.8 + - + +
157A ARG* 3.5 2.4 + - - +
158A ALA* 2.9 34.1 + - + +
264A LEU* 4.7 0.9 - - + -
332A ARG 4.6 1.3 - - - +
333A LEU* 5.0 2.0 - - + -
335A TYR* 3.5 47.4 - - + +
336A PHE* 3.7 21.3 - - + +
339A TYR* 3.7 34.3 - - + -
473A LEU* 4.4 12.8 - - - -
477A ILE* 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLY 3.0 19.6 + - - +
152A PRO 4.0 0.2 - - - +
154A MSE 1.3 94.0 - - + +
156A VAL* 1.3 66.8 + - - +
158A ALA* 3.2 3.5 + - - -
159A LEU* 2.9 48.2 + - + +
264A LEU* 4.1 16.6 - - + -
272A ILE* 3.8 34.1 - - + -
276A ILE* 5.6 0.2 - - - +
284A LEU* 4.1 8.3 - - + -
473A LEU* 4.0 10.3 - - + -
477A ILE* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO 2.9 20.8 + - - +
153A LYS 4.0 2.7 - - - +
155A VAL* 1.3 76.9 - - - +
157A ARG* 1.3 62.2 + - - +
159A LEU* 3.6 1.7 + - - -
160A GLN* 3.3 7.4 + - - -
163A HIS* 2.8 48.3 + - + +
169A VAL* 4.8 9.2 - - + +
171A PHE* 3.9 24.2 - - + -
271A SER 3.8 8.7 - - - +
272A ILE* 3.8 29.6 - - + +
275A ALA* 4.0 10.3 - - + -
276A ILE* 5.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS 3.1 17.2 + - - +
154A MSE 3.8 3.1 - - - +
156A VAL* 1.3 78.5 - - - +
158A ALA* 1.3 63.6 + - - +
160A GLN* 3.1 49.6 + - - +
331A GLU* 4.2 21.0 + - - +
332A ARG* 3.7 27.4 - - - +
334A CYS* 3.7 29.9 - - - -
335A TYR* 3.8 17.5 - - + -
601A MES 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MSE 2.9 22.0 + - - +
155A VAL* 3.2 1.3 + - - +
157A ARG* 1.3 76.5 - - - +
159A LEU* 1.3 60.8 + - - +
161A PRO* 4.2 0.7 - - - +
332A ARG* 3.1 40.9 + - - +
333A LEU* 4.2 16.8 - - + -
468A LEU* 3.6 13.5 - - + +
473A LEU* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 2.9 37.6 + - + +
156A VAL 3.7 3.4 - - - -
158A ALA* 1.3 84.2 - - + +
160A GLN* 1.3 63.1 + - - +
161A PRO* 3.2 6.1 - - - -
162A TYR* 2.9 26.5 + - + +
163A HIS* 3.4 7.5 - - - -
276A ILE* 3.7 32.5 - - + -
284A LEU* 4.6 4.0 - - + -
468A LEU* 4.4 4.5 - - + +
469A SER* 3.6 13.2 - - - +
470A PRO* 3.6 40.2 - - + -
473A LEU* 3.8 15.5 - - + -
----------------------------------------------------------
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