Contacts of the helix formed by residues 131 - 146 (chain E) in PDB entry 5WC9
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 GLU 131 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E LEU* 1.3 78.2 - - - +
132E LYS* 1.3 66.9 + - - +
133E GLU* 3.3 10.9 - - + +
134E VAL* 3.1 37.4 - - + +
135E VAL* 3.4 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 3.9 13.3 - - + +
122E MET* 4.1 24.4 - - + +
125E ALA* 4.1 11.1 - - - +
130E LEU 3.8 0.8 + - - -
131E GLU* 1.3 74.4 - - - +
133E GLU* 1.3 62.4 + - - +
135E VAL 3.5 0.9 + - - -
136E ARG* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E GLU* 3.3 8.6 - - + +
132E LYS* 1.3 80.0 - - - +
134E VAL* 1.3 67.3 + - + +
136E ARG* 3.0 40.9 + - - +
137E VAL* 2.9 38.2 + - + +
185G T 5.2 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E THR* 4.2 12.1 - - + +
98E ILE* 5.3 9.8 - - + +
130E LEU* 3.8 22.9 - - + -
131E GLU* 3.1 46.0 - - + +
133E GLU* 1.3 77.9 - - + +
135E VAL* 1.3 58.6 + - + +
137E VAL* 3.7 3.5 + - - +
138E TRP* 3.0 28.1 + - - +
183G C 5.8 0.2 - - - -
184G A 3.4 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE* 6.4 0.7 - - + -
106E LEU* 3.9 17.0 - - + -
121E ILE* 4.4 20.9 - - + +
124E MET* 4.7 7.2 - - + -
125E ALA* 4.1 13.9 - - + +
128E LEU* 5.2 0.9 - - + -
130E LEU* 3.9 28.0 - - + -
131E GLU 3.4 16.4 - - - +
132E LYS 3.5 3.9 + - - +
133E GLU 3.2 0.6 - - - -
134E VAL* 1.3 76.7 - - + +
136E ARG* 1.3 66.0 + - - +
138E TRP* 3.3 5.5 + - - +
139E PHE* 3.2 45.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 4.0 30.1 - - + +
132E LYS 3.0 14.0 + - - +
133E GLU* 3.0 41.3 + - - +
135E VAL* 1.3 79.2 - - - +
137E VAL* 1.3 74.8 + - - +
139E PHE* 3.3 4.0 + - - +
140E CYS* 3.1 43.9 + - - -
143E ARG* 4.9 1.4 + - - +
185G T 5.6 4.9 - - - +
171H C 5.5 5.1 + - - -
172H G 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E GLU* 2.9 40.9 + - + +
134E VAL* 4.3 4.9 - - - +
136E ARG* 1.3 81.2 - - - +
138E TRP* 1.3 58.5 + - - +
140E CYS* 3.1 10.7 + - + -
141E ASN* 2.8 51.1 + - - +
183G C 6.1 1.3 - - + -
184G A 4.0 17.7 - - + +
185G T 3.6 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E ILE* 3.9 17.1 - - + +
103E LYS* 4.5 14.1 - - + +
106E LEU* 3.6 47.3 - - + +
107E GLU* 3.6 30.5 - - + -
110E PHE* 4.4 0.9 - - + -
134E VAL 3.0 20.1 + - - +
135E VAL* 3.5 10.1 - - - +
136E ARG 3.2 0.2 - - - -
137E VAL* 1.3 78.2 - - - +
139E PHE* 1.3 75.1 + + - +
141E ASN* 3.3 5.4 + - + +
142E ARG* 2.7 59.8 + - + +
183G C 3.7 25.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU* 3.8 24.0 - - + -
109E HIS* 4.4 3.1 - - + -
110E PHE* 3.7 36.0 - + + -
113E GLN 4.0 14.1 - - - -
114E ASN 4.1 0.2 - - - -
116E PRO* 3.8 28.5 - - + -
121E ILE* 5.0 4.0 - - + -
124E MET* 3.7 26.2 - - + -
135E VAL* 3.2 43.0 + - + -
136E ARG* 3.3 6.3 + - - +
138E TRP* 1.3 88.2 - + - +
140E CYS* 1.3 52.2 + - - +
142E ARG* 3.5 3.1 - - - +
143E ARG* 2.7 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ARG* 3.1 49.8 + - - -
137E VAL* 3.1 15.3 + - + +
139E PHE* 1.3 74.8 - - - +
141E ASN* 1.3 61.6 + - - +
143E ARG* 3.0 28.0 + - - +
144E GLN* 2.8 35.1 + - + +
172H G 5.5 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E VAL* 2.8 31.3 + - - +
138E TRP* 3.9 4.8 - - - +
140E CYS* 1.3 73.8 - - - +
142E ARG* 1.3 61.7 + - - +
144E GLN* 3.5 10.7 + - - +
145E ARG* 3.0 24.1 + - - +
183G C 3.2 25.7 - - + +
184G A 2.8 51.1 + - - +
185G T 5.3 0.5 - - - +
174H A 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E GLU* 2.2 49.5 + - - -
110E PHE* 3.5 35.7 - - + -
138E TRP* 2.7 39.6 + - + +
139E PHE* 3.5 10.5 - - - +
140E CYS 3.2 0.2 - - - -
141E ASN* 1.3 75.0 - - - +
143E ARG* 1.3 62.1 + - - +
145E ARG* 3.3 32.4 + - - +
146E GLU* 3.5 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E PHE* 3.9 20.6 - - + -
114E ASN* 3.4 16.7 + - + +
115E LYS* 3.4 40.3 - - - +
116E PRO* 4.0 18.4 + - - +
121E ILE* 5.6 4.2 - - - +
136E ARG* 4.9 1.4 + - - +
139E PHE* 2.7 30.2 + - - +
140E CYS* 3.4 29.4 - - - +
142E ARG* 1.3 74.3 - - - +
144E GLN* 1.3 64.5 + - + +
145E ARG 3.2 0.9 + - - -
146E GLU* 3.2 15.8 + - - +
147E LYS* 3.6 11.1 + - - +
171H C 5.2 0.8 - - - -
172H G 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E CYS* 2.8 22.3 + - + +
141E ASN* 3.8 12.3 - - - +
143E ARG* 1.3 78.5 - - + +
145E ARG* 1.3 57.5 + - - +
147E LYS* 3.0 32.5 + - - +
148E ARG* 3.9 4.9 + - - +
172H G 3.4 14.6 - - + +
173H A 2.7 65.8 + - - +
174H A 4.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ASN 3.0 17.1 + - - +
142E ARG* 3.5 30.6 - - - +
143E ARG 3.1 0.6 - - - -
144E GLN* 1.3 73.0 - - - +
146E GLU* 1.3 59.4 + - + +
147E LYS 3.1 5.2 - - - -
148E ARG* 3.2 58.7 - - - +
182G T 2.7 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E PHE* 4.7 10.9 - - + -
114E ASN* 6.3 0.4 - - - +
142E ARG* 3.5 34.7 + - - +
143E ARG* 3.2 10.7 + - - +
145E ARG* 1.3 77.9 - - - +
147E LYS* 1.3 56.4 + - - +
148E ARG 3.3 7.2 + - - +
----------------------------------------------------------
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