Contacts of the helix formed by residues 114 - 128 (chain E) in PDB entry 1MDU
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 114 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ILE* 4.4 14.8 - - + -
112E LEU 3.4 8.5 - - - +
113E ASN* 1.3 96.3 - - - +
115E LYS* 1.3 66.4 + - - +
116E ALA* 4.4 6.3 - - + +
117E ASN* 2.9 38.0 + - - +
118E ARG* 3.3 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ASN 3.5 2.3 + - - +
114E PRO* 1.3 70.8 - - - +
116E ALA* 1.3 56.8 - - - +
118E ARG* 3.2 12.0 + - - +
119E GLU* 3.0 35.3 + - - +
373E HIS* 3.4 44.4 - - + +
374E ARG 5.9 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E PRO* 3.2 4.4 - - + +
115E LYS* 1.3 77.4 - - - +
117E ASN* 1.3 62.6 + - - +
119E GLU* 3.4 13.1 + - - +
120E LYS* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E ILE* 3.6 16.2 - - - +
78E ILE* 3.2 29.2 + - + +
81E TRP* 3.5 23.2 - - + +
113E ASN* 3.5 19.6 + - - +
114E PRO* 2.9 29.8 + - - +
116E ALA* 1.3 78.2 - - - +
118E ARG* 1.3 66.5 + - - +
120E LYS 3.1 0.7 + - - -
121E MET* 2.9 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E GLU* 2.9 41.6 + - - +
113E ASN* 3.7 10.1 - - - +
114E PRO 3.5 12.1 - - - +
115E LYS* 3.2 21.5 + - - +
117E ASN* 1.3 75.7 - - - +
119E GLU* 1.3 61.8 + - - +
121E MET* 3.2 14.9 + - - +
122E THR* 2.9 28.6 + - - -
136E VAL* 3.7 31.8 + - - +
137E ALA* 5.5 0.4 - - - +
138E ILE* 5.6 3.0 - - - +
372E VAL* 3.1 40.0 + - + +
373E HIS* 4.0 11.7 - - - -
374E ARG* 5.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E LYS* 3.0 19.5 + - - +
116E ALA* 3.4 12.2 - - - +
118E ARG* 1.3 78.1 - - - +
120E LYS* 1.3 61.9 + - - +
122E THR* 3.3 6.6 + - - -
123E GLN* 3.2 19.6 + - - +
369E PRO* 3.7 33.6 - - + +
370E SER* 4.7 8.0 - - - -
372E VAL* 4.4 1.6 - - + -
373E HIS* 2.7 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E TRP* 3.7 56.7 - - + +
116E ALA 2.8 20.1 + - - +
117E ASN 3.1 3.3 + - - +
119E GLU* 1.3 70.4 - - - +
121E MET* 1.3 67.1 + - - +
123E GLN* 3.4 24.5 - - - +
124E ILE* 3.3 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ASN* 5.9 0.7 - - - +
78E ILE* 4.0 17.3 - - + -
81E TRP* 3.6 22.6 - - + -
88E TRP* 4.4 12.7 - - + -
107E LEU* 4.0 31.0 - - + -
108E THR 3.8 21.5 - - - +
109E GLU* 4.5 8.1 - - - +
113E ASN* 4.2 13.9 - - - -
117E ASN* 2.9 24.1 + - - +
118E ARG* 3.2 15.9 + - - +
120E LYS* 1.3 77.5 - - - +
122E THR* 1.3 63.5 + - - +
124E ILE* 3.3 3.9 + - - +
125E MET* 3.1 26.9 + - - +
134E MET* 4.8 3.4 - - + -
136E VAL* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ARG 2.9 10.9 + - - -
119E GLU* 3.4 9.9 - - - -
120E LYS 3.2 0.2 - - - -
121E MET* 1.3 75.5 - - - +
123E GLN* 1.3 67.5 + - - +
125E MET* 3.2 2.6 + - - +
126E PHE* 3.1 49.8 + - + -
134E MET* 3.6 16.4 - - - +
136E VAL* 4.9 0.7 - - - +
359E ILE* 5.6 0.7 - - + -
364E TYR* 4.0 14.1 - - + -
369E PRO* 4.5 4.7 - - + -
371E ILE* 5.8 0.4 - - + -
372E VAL* 2.7 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E GLU 3.2 6.4 + - - +
120E LYS* 3.4 37.3 - - - +
122E THR* 1.3 78.6 - - - +
124E ILE* 1.3 64.3 + - + +
127E GLU* 2.6 59.8 + - - +
364E TYR* 3.2 24.6 + - - +
369E PRO* 4.3 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E TRP* 3.8 42.2 - - + +
85E GLU* 3.8 26.7 - - + +
88E TRP* 4.1 15.5 - - + -
120E LYS* 3.3 20.1 + - + +
121E MET 3.7 7.0 - - - +
122E THR 3.2 0.8 - - - -
123E GLN* 1.3 83.3 - - + +
125E MET* 1.3 63.1 + - - +
128E THR* 2.8 36.2 + - - +
129E PHE* 3.1 30.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E TRP* 3.4 54.5 - - + -
92E PHE* 4.2 15.0 - - + -
105E THR* 4.8 4.3 - - - -
107E LEU* 3.5 34.1 - - + -
121E MET 3.1 12.5 + - - +
122E THR 3.7 7.2 - - - +
124E ILE* 1.3 76.5 - - - +
126E PHE* 1.3 57.4 + - - +
129E PHE* 3.4 17.9 - - + +
130E ASN 2.9 22.2 + - - -
131E VAL* 3.1 36.1 + - + +
134E MET* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E THR* 3.1 40.5 + - + +
125E MET* 1.3 78.3 - - - +
127E GLU* 1.3 60.6 + - - +
130E ASN* 3.0 27.9 + - - +
131E VAL* 3.5 30.5 - - + +
133E ALA* 4.1 3.6 - - - -
134E MET* 3.8 17.5 - - + -
359E ILE* 3.4 28.5 - - + -
360E THR 3.8 7.9 - - - -
361E LYS* 3.5 42.3 - - + -
364E TYR* 3.4 43.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E GLN* 2.6 40.3 + - + +
124E ILE* 5.1 0.2 - - - -
126E PHE* 1.3 74.6 - - - +
128E THR* 1.3 64.4 + - - +
130E ASN* 3.7 10.3 - - - +
361E LYS* 6.2 1.3 - - - +
364E TYR* 2.4 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E GLU* 3.5 39.7 + - + +
124E ILE* 2.8 31.3 + - - +
127E GLU* 1.3 77.3 - - - +
129E PHE* 1.3 74.9 + - + +
130E ASN* 3.6 4.0 - - - +
----------------------------------------------------------
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