Contacts of the helix formed by residues 94 - 108 (chain F) in PDB entry 3MIW
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 MET 94 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ILE* 1.3 62.6 + - - +
96F GLU* 3.7 5.8 - - + +
97F GLN* 3.0 34.5 + - + +
98F GLN* 2.9 33.9 + - - +
96H GLU* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 5.5 8.4 - - + +
94F MET* 1.3 80.5 - - - +
96F GLU* 1.3 61.6 + - - +
97F GLN 3.4 0.2 - - - -
98F GLN* 3.8 9.3 + - - +
99F MET* 3.3 26.7 + - - +
95H ILE* 5.9 4.7 - - + -
96H GLU* 3.7 12.2 + - + -
99H MET* 5.0 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D MET 5.9 5.2 - - - +
95D ILE* 6.0 10.3 - - + +
98D GLN* 3.8 14.4 + - - +
94F MET* 4.4 3.2 - - + +
95F ILE* 1.3 75.6 - - - +
97F GLN* 1.3 77.2 + - + +
99F MET* 3.2 9.5 - - - +
100F ASP* 2.9 50.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F MET* 3.0 31.4 + - + +
95F ILE 4.4 0.6 - - - +
96F GLU* 1.3 87.2 - - + +
98F GLN* 1.3 58.3 + - + +
100F ASP* 2.6 40.5 + - + +
101F ARG* 3.0 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F MET 2.9 29.9 + - - +
95F ILE* 4.1 3.6 - - - +
96F GLU 3.4 0.4 - - - -
97F GLN* 1.3 76.2 - - + +
99F MET* 1.3 61.8 + - - +
101F ARG* 3.3 8.8 + - - +
102F ILE* 3.2 26.0 + - - +
96H GLU* 3.5 22.7 + - - +
99H MET* 3.0 37.2 - - + +
100H ASP* 2.7 39.6 + - - +
103H VAL* 4.4 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 3.8 17.9 - - + +
98D GLN* 3.0 56.8 - - + +
99D MET* 3.4 33.2 - - - +
102D ILE* 3.8 22.4 - - + -
95F ILE 3.3 14.7 + - - +
96F GLU* 3.2 6.5 + - - +
97F GLN 3.1 0.2 - - - -
98F GLN* 1.3 79.2 - - - +
100F ASP* 1.3 62.0 + - - +
102F ILE* 3.4 14.3 + - - +
103F VAL* 3.0 28.9 + - - +
99H MET* 5.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLN* 2.9 24.0 + - - +
96F GLU* 2.9 34.7 + - - +
97F GLN* 2.6 26.5 + - + +
99F MET* 1.3 71.8 - - - +
101F ARG* 1.3 54.1 + - - +
103F VAL* 3.2 10.7 - - - +
104F LYS* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F GLN 3.0 8.5 + - - +
98F GLN* 3.8 10.1 - - - +
99F MET 3.3 0.2 - - - -
100F ASP* 1.3 71.6 - - - +
102F ILE* 1.3 52.7 + - - +
103F VAL 2.8 4.9 - - - -
104F LYS* 2.7 10.7 + - - +
105F GLU* 2.5 40.5 + - + +
103H VAL* 4.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ILE* 4.3 27.3 - - + +
98F GLN 3.2 9.7 + - - +
99F MET* 3.4 14.3 + - - +
101F ARG* 1.3 78.5 - - - +
103F VAL* 1.3 54.9 + - - +
105F GLU* 3.6 10.0 + - - +
106F MET* 3.2 25.9 + - + +
99H MET* 4.3 20.4 - - - -
102H ILE* 4.0 24.0 - - + +
103H VAL* 3.4 35.7 - - + -
106H MET* 5.0 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLN* 5.0 16.6 - - + +
101D ARG* 5.3 19.3 - - + +
102D ILE* 4.6 19.5 - - + -
99F MET* 3.0 21.5 - - + +
100F ASP* 3.2 13.7 - - - +
101F ARG 2.8 0.4 - - - -
102F ILE* 1.3 78.1 - - + +
104F LYS* 1.3 62.2 + - - +
105F GLU 3.0 1.1 - - - -
106F MET* 3.4 12.1 + - - +
107F ARG* 3.4 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ASP 3.1 11.7 + - - +
101F ARG* 2.7 14.4 + - - +
103F VAL* 1.3 75.4 - - - +
105F GLU* 1.3 57.3 + - - +
106F MET 3.3 0.9 - - - -
107F ARG* 3.3 24.6 + - - +
108F ARG* 3.0 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F ARG* 2.5 16.9 + - - +
102F ILE* 3.7 11.7 - - - +
104F LYS* 1.3 77.9 - - - +
106F MET* 1.3 56.9 + - - +
107F ARG 3.5 0.4 - - - -
108F ARG* 2.8 33.3 + - - +
109F GLN* 3.9 19.6 + - - +
103H VAL* 4.8 12.3 - - + +
106H MET* 4.0 30.5 - - + +
107H ARG* 4.3 15.6 - - - +
110H LEU* 3.4 30.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ILE* 6.2 6.7 - - + -
105D GLU* 4.8 14.1 - - + +
109D GLN* 5.0 4.7 - - - +
102F ILE* 3.2 17.1 + - + +
103F VAL* 3.4 6.9 + - - +
104F LYS 3.3 0.4 - - - -
105F GLU* 1.3 76.7 - - - +
107F ARG* 1.3 61.7 + - - +
108F ARG 3.2 1.1 - - - -
109F GLN* 4.0 14.3 - - - +
110F LEU* 3.2 28.8 + - - +
106H MET* 5.5 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D GLU* 5.2 5.2 - - - +
8F EDO 3.7 30.3 + - - -
103F VAL 3.4 10.6 + - - +
104F LYS* 3.3 21.4 + - - +
106F MET* 1.3 78.0 - - - +
108F ARG* 1.3 83.2 + - - +
110F LEU* 3.4 7.7 - - - +
111F GLU* 2.8 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F EDO 3.7 28.9 + - - -
104F LYS* 3.0 33.4 + - - +
105F GLU* 2.8 43.9 + - - +
107F ARG* 1.3 102.9 - - - +
109F GLN* 1.3 65.0 + - - +
110F LEU 3.1 0.2 - - - -
111F GLU* 3.0 7.9 + - - +
112F MET* 3.0 23.7 + - - +
110H LEU* 4.3 23.3 - - + +
----------------------------------------------------------
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