Contacts of the helix formed by residues 128 - 140 (chain E) in PDB entry 4LQL
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 HIS 128 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D GLU* 4.0 15.4 + - - -
332D ASP 3.4 21.3 + - - +
333D TYR* 3.5 21.8 + + - -
446D HIS* 3.4 29.9 - + + +
83E PHE* 3.3 39.9 - + + +
125E GLN* 2.9 64.6 + - + -
127E ALA* 1.3 79.0 - - - +
129E GLY* 1.3 56.8 + - - +
130E ASP 3.6 2.2 - - - -
131E ARG* 3.6 9.9 - - - +
132E GLU* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E MET* 3.0 28.1 - - - +
82E THR 3.2 21.5 + - - -
83E PHE* 3.7 15.3 - - - -
84E SER 4.4 5.0 + - - +
125E GLN 4.0 0.4 + - - -
126E SER 3.7 3.6 + - - -
128E HIS* 1.3 77.3 - - - +
130E ASP* 1.3 58.3 + - - +
131E ARG 3.2 4.3 - - - -
132E GLU* 4.2 3.3 - - - +
133E TYR 3.7 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D MET* 4.3 7.4 - - - +
79E TRP* 4.7 3.4 - - + +
80E MET* 4.2 21.9 + - + +
102E HIS* 4.1 21.1 - - + -
104E ALA* 4.5 20.2 - - + +
105E THR 5.5 0.2 - - - +
126E SER* 3.6 14.7 + - - +
129E GLY* 1.3 76.7 - - - +
131E ARG* 1.3 59.8 + - - +
133E TYR* 4.3 6.1 - - - -
134E ALA* 3.4 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D VAL* 4.4 0.6 - - - +
332D ASP* 3.8 23.3 + - - +
344D ILE* 6.0 1.4 - - - +
432D LEU* 6.3 1.6 - - - +
435D GLY 4.6 7.9 + - - -
436D ALA* 4.7 10.9 - - - +
439D TRP* 2.8 46.5 - - + +
440D MET* 4.5 10.3 - - + +
444D GLY 3.6 14.4 - - - +
445D GLY* 3.4 20.6 + - - +
446D HIS* 4.8 1.6 - - - +
127E ALA* 2.3 42.1 + - - +
128E HIS* 3.6 12.6 - - - +
129E GLY 3.2 0.4 - - - -
130E ASP* 1.3 82.3 - - - +
132E GLU* 1.3 60.0 + - - +
133E TYR 3.2 0.7 - - - -
134E ALA* 3.3 7.3 - - + +
135E TYR* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D VAL* 3.9 4.8 - - - +
189D ALA* 3.0 18.3 + - - +
190D VAL* 2.7 46.9 + - + +
446D HIS* 3.8 7.9 + - + -
83E PHE* 3.5 25.4 - - + -
84E SER 3.2 10.7 - - - +
85E PRO* 3.0 11.4 - - - +
86E ALA* 2.3 52.1 + - - +
128E HIS 3.3 12.0 + - - +
129E GLY 4.6 1.8 - - - +
131E ARG* 1.3 77.9 - - - +
133E TYR* 1.3 63.6 + - - +
135E TYR* 3.6 2.3 + - - +
136E ILE 3.5 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E THR* 4.3 13.2 - - - -
80E MET* 3.7 31.6 - - + -
84E SER 4.8 2.0 + - - +
86E ALA* 4.4 6.9 - - - +
89E TRP* 4.9 18.4 - + + +
102E HIS* 4.9 12.1 - + + -
129E GLY 3.7 8.8 + - - +
130E ASP* 4.3 3.8 - - - -
131E ARG 3.2 0.2 - - - -
132E GLU* 1.3 75.1 - - - +
134E ALA* 1.3 71.7 + - - +
136E ILE* 2.9 27.4 - - + +
137E ASN* 3.6 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D MET* 3.9 32.8 - - + +
443D GLY 5.2 2.2 - - - +
444D GLY 5.3 0.9 - - - +
102E HIS* 5.0 8.5 - - + -
130E ASP 3.4 20.0 + - - +
131E ARG* 3.3 13.5 + - - +
133E TYR* 1.3 77.7 - - - +
135E TYR* 1.3 52.5 + - - +
137E ASN* 2.5 41.3 + - - +
138E SER* 3.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ALA* 5.4 3.4 - - + -
190D VAL* 3.5 46.4 - - + -
394D SER* 6.1 2.7 - - - -
395D TYR 6.2 0.4 - - - -
396D PHE* 6.6 0.2 - + - -
443D GLY* 3.7 25.2 + - - +
444D GLY 4.3 0.2 - - - +
131E ARG 2.8 13.7 + - - +
132E GLU 3.9 0.2 - - - +
133E TYR 3.5 0.2 - - - -
134E ALA* 1.3 70.8 - - - +
136E ILE* 1.3 71.1 + - + +
137E ASN 3.0 0.9 + - - -
138E SER* 3.2 10.8 + - - +
139E ARG* 3.1 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B VAL* 4.3 12.6 - - + -
200B ILE* 6.1 0.9 - - + -
189D ALA* 4.5 11.4 - - + -
86E ALA* 4.0 19.0 - - + +
89E TRP* 4.8 9.0 - - + -
90E ILE* 3.5 44.6 - - + -
93E THR* 4.6 16.8 - - - +
132E GLU 3.5 3.4 + - - -
133E TYR* 2.9 30.1 - - + +
134E ALA 2.9 2.4 + - - -
135E TYR* 1.3 79.1 - - + +
137E ASN* 1.3 60.3 + - + +
139E ARG* 3.7 7.8 - - + +
140E LEU* 2.8 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E THR* 5.9 3.4 - - - +
100E LEU* 6.0 5.8 - - + -
133E TYR 4.4 4.0 - - - +
134E ALA* 2.5 24.3 + - - +
136E ILE* 1.3 73.9 - - + +
138E SER* 1.3 52.3 + - - +
139E ARG 2.2 20.9 + - - -
140E LEU* 2.7 24.5 + - - +
141E ASN 3.3 1.0 + - - -
142E VAL* 3.7 24.6 + - + +
144E ALA* 5.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D PHE* 5.4 5.5 - - - +
440D MET 4.7 5.1 + - - -
441D LYS 3.1 30.3 - - - -
442D TYR* 3.9 0.8 - - - -
443D GLY* 3.5 27.3 + - - -
134E ALA 3.3 5.5 + - - -
135E TYR* 3.2 9.4 + - - -
137E ASN* 1.3 72.6 - - - +
139E ARG* 1.3 55.6 + - - +
141E ASN* 4.3 12.6 + - - +
142E VAL 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ASP* 3.2 23.2 + - - -
196B VAL* 4.2 16.3 - - + +
197B ALA* 4.1 10.5 - - - +
200B ILE* 3.9 25.9 - - + +
193D GLY* 5.7 0.8 - - - -
395D TYR* 2.7 34.3 + - - +
396D PHE* 3.2 28.5 - - + +
397D ASP* 4.0 22.1 - - - +
443D GLY* 6.6 0.2 - - - -
135E TYR* 3.1 25.4 - - + +
136E ILE* 3.7 9.0 - - + +
137E ASN 2.2 17.0 + - - -
138E SER* 1.3 68.9 - - - +
140E LEU* 1.3 59.7 + - + +
141E ASN* 3.0 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ILE* 4.8 24.7 - - + -
90E ILE* 5.3 8.1 - - + +
93E THR* 5.1 19.2 - - - +
94E GLU* 5.6 4.3 - - + -
136E ILE* 2.8 35.2 + - + +
137E ASN* 2.7 9.8 + - - +
139E ARG* 1.3 72.2 - - + +
141E ASN* 1.3 51.5 + - - +
142E VAL* 2.4 29.0 + - + +
----------------------------------------------------------
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