Contacts of the helix formed by residues 80 - 92 (chain A) in PDB entry 1M1I
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 GLY 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 4.3 4.8 - - - +
79A ILE* 1.4 88.5 - - - +
81A VAL* 1.3 54.9 + - - -
82A GLU 3.1 4.0 - - - -
83A LYS* 3.0 22.8 + - - +
84A PHE* 2.7 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 3.1 11.1 + - - +
80A GLY* 1.3 68.4 - - - -
82A GLU* 1.3 68.2 + - + +
84A PHE* 3.2 2.9 + - - +
85A LEU* 3.0 28.9 + - - +
107A PHE* 3.8 35.6 - - + -
111A VAL* 3.7 31.2 - - + -
113A GLY 4.4 0.4 - - - +
114A LEU* 4.0 22.2 - - + -
146A ILE* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 3.1 0.8 - - - -
81A VAL* 1.3 87.5 - - + +
83A LYS* 1.3 63.4 + - + +
85A LEU* 3.4 7.3 + - - +
86A GLU* 3.0 38.5 + - - +
114A LEU* 2.7 45.6 - - + +
116A TRP* 5.3 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 5.5 17.1 - - + -
77A PRO* 5.6 13.8 - - + +
80A GLY* 3.0 20.4 + - - +
82A GLU* 1.3 76.0 - - + +
84A PHE* 1.3 53.8 + - - +
86A GLU* 3.4 16.0 + - - +
87A LEU* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 4.5 9.4 - - + -
76A PHE* 3.5 28.5 - + + -
79A ILE 4.2 9.2 - - - +
80A GLY 2.7 19.0 + - - +
81A VAL* 3.2 6.9 + - - +
83A LYS* 1.3 70.7 - - - +
85A LEU* 1.3 56.5 + - - +
87A LEU* 3.3 7.4 + - + +
88A ASN* 2.7 41.5 + - + +
101A VAL* 3.5 34.5 - - + -
103A THR* 4.7 4.7 - - + -
105A ARG* 2.7 36.8 - - - -
107A PHE* 4.8 7.9 - + + -
146A ILE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 3.0 15.7 + - - +
82A GLU* 3.8 7.9 - - - +
83A LYS 3.4 0.2 - - - -
84A PHE* 1.3 75.0 - - - +
86A GLU* 1.3 54.4 + - + +
88A ASN* 3.3 4.8 + - - +
89A SER* 2.8 35.7 + - - -
114A LEU* 4.1 13.5 - - + -
115A ALA* 3.9 28.5 - - - +
116A TRP* 3.9 31.2 - - + +
144A THR* 3.3 27.1 - - + +
145A GLY* 3.6 11.2 - - - +
146A ILE* 3.3 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.0 25.5 + - - +
83A LYS* 3.6 19.3 + - - +
85A LEU* 1.3 76.1 - - + +
87A LEU* 1.3 56.4 + - - +
89A SER* 3.3 8.9 + - - -
90A GLU* 3.0 29.7 + - - +
116A TRP* 4.2 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 4.4 11.2 - - - +
74A PHE* 4.3 28.9 - - + -
76A PHE* 3.6 36.1 - - + -
83A LYS 2.8 22.9 + - - +
84A PHE* 3.5 7.9 - - + +
86A GLU* 1.3 71.0 - - - +
88A ASN* 1.3 64.6 + - - +
90A GLU* 3.2 11.5 + - + +
91A GLN* 3.0 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.2 7.2 + - - -
84A PHE* 2.7 31.3 + - + +
85A LEU* 3.4 7.2 - - - +
87A LEU* 1.3 72.1 - - - +
89A SER* 1.3 56.7 + - - +
91A GLN* 3.2 6.1 + - - +
92A ASN* 2.9 47.3 + - - +
101A VAL* 2.9 41.5 - - + +
144A THR* 3.1 26.7 + - - +
145A GLY 4.3 2.0 + - - -
146A ILE* 4.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 2.8 11.5 + - - -
86A GLU* 3.4 9.6 - - - -
88A ASN* 1.3 76.8 - - - +
90A GLU* 1.3 59.2 + - - +
92A ASN 2.6 24.5 - - - +
93A HIS* 2.8 16.7 - - - -
116A TRP* 3.9 7.7 + - - -
134A TYR* 5.5 5.6 - - - -
141A SER* 4.4 3.4 - - - -
142A LEU* 5.0 15.0 - - - -
143A ASN 5.1 0.2 - - - -
144A THR* 2.8 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 3.0 13.5 + - - +
87A LEU* 3.5 16.1 - - + +
89A SER* 1.3 76.7 - - - +
91A GLN* 1.3 73.3 + - + +
93A HIS* 3.1 10.7 + - - -
134A TYR* 5.7 7.2 - - + -
136A ASP 5.4 7.0 - - - +
137A GLY* 5.9 1.6 - - - -
139A LYS* 2.6 48.3 + - + +
141A SER* 4.3 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.0 36.6 + - + +
88A ASN* 3.7 4.0 - - - +
90A GLU* 1.3 95.2 + - - +
92A ASN* 1.3 73.9 + - - +
93A HIS* 4.7 2.2 - - - -
139A LYS* 4.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.8 25.5 + - + -
11A GLN* 4.7 15.8 + - - +
60A ARG* 5.6 2.8 + - - -
62A ASN* 6.2 0.2 - - - +
88A ASN* 2.9 32.4 + - - +
89A SER* 2.6 27.0 - - - +
90A GLU 3.4 0.2 - - - -
91A GLN* 1.3 93.4 - - - +
93A HIS* 1.3 68.9 + - - +
94A ASP* 5.2 0.2 - - - -
101A VAL* 5.2 0.4 - - - +
142A LEU 4.4 2.3 - - - +
143A ASN* 5.7 0.7 - - - +
----------------------------------------------------------
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