Contacts of the strand formed by residues 150 - 159 (chain G) in PDB entry 1M06
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 ASN 150 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LYS* 3.8 19.4 + - + +
72G THR* 6.2 0.9 - - - -
103G GLU* 3.2 7.1 - - - +
104G SER 3.0 32.3 + - - +
105G ALA* 3.5 16.6 + - - +
106G SER 3.5 17.1 + - - -
107G GLU* 3.7 30.1 + - - +
148G GLY 5.3 1.6 + - - -
149G ASN* 1.3 77.9 - - - +
151G VAL* 1.3 63.7 + - - +
152G PHE* 3.7 17.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G LYS* 3.7 6.3 - - - +
70G VAL* 2.8 49.5 + - + +
72G THR* 4.7 9.0 - - + +
101G ARG* 3.6 35.0 - - + +
102G PHE 4.1 2.0 - - - +
103G GLU* 4.0 6.7 - - + -
141G ASP 4.9 0.7 - - - +
142G ILE* 3.9 13.2 - - - +
144G PRO* 3.5 39.0 - - + -
150G ASN* 1.3 75.6 - - - +
152G PHE* 1.3 67.5 + - - +
153G VAL* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G SER* 4.8 10.3 - - - -
67G ALA* 4.7 4.0 - - + -
68G MET* 3.6 7.2 - - - +
69G LYS* 3.8 33.2 - - + -
101G ARG* 3.3 2.6 - - - +
102G PHE* 2.9 75.0 + + + +
104G SER* 4.0 5.2 - - - -
106G SER 3.6 16.8 - - - -
107G GLU* 3.6 15.0 - - - -
109G PRO* 3.4 32.5 - - + -
150G ASN* 3.7 28.0 - - + -
151G VAL* 1.3 74.6 - - - +
153G VAL* 1.3 70.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.9 10.1 - - - +
67G ALA* 4.4 3.6 - - - -
68G MET* 2.7 34.8 + - - +
70G VAL* 3.4 24.9 - - + +
81G ILE* 3.3 48.0 - - + -
99G ILE* 4.0 6.5 - - + -
100G VAL* 3.1 15.0 - - - +
101G ARG* 4.3 13.5 - - + -
102G PHE* 5.4 0.7 - - - -
140G VAL* 4.6 3.6 - - + -
151G VAL* 4.6 1.6 - - + -
152G PHE* 1.3 81.6 - - - +
154G GLY* 1.3 64.4 + - - +
173G THR* 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G VAL 3.2 13.9 - - - -
67G ALA* 4.1 2.0 - - - -
68G MET* 4.6 1.6 - - - -
99G ILE* 3.3 8.1 - - - +
100G VAL* 2.6 43.3 + - - +
153G VAL* 1.3 83.4 - - - +
155G VAL* 1.3 59.1 + - - -
173G THR* 4.5 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G PHE 4.3 0.2 - - - +
65G ILE* 3.7 2.7 - - - +
66G VAL* 3.0 31.8 + - + +
83G ALA* 4.4 20.0 - - + -
85G VAL* 4.0 21.8 - - + -
97G VAL* 4.1 13.5 - - + -
98G GLY 3.1 13.2 - - - +
99G ILE* 4.4 0.9 - - + +
122G ILE* 6.1 1.3 - - + -
154G GLY* 1.3 73.3 - - - -
156G ILE* 1.3 75.6 + - - +
157G CYS* 4.7 1.6 - - + +
171G ILE* 3.0 35.7 - - + -
173G THR* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ILE* 5.0 5.6 - - + -
63G SER* 3.6 27.6 - - - +
64G PHE 3.5 12.3 - - - +
65G ILE* 3.8 20.9 - - + -
96G ILE 3.6 0.2 - - - +
97G VAL* 3.1 23.3 - - - -
98G GLY* 2.8 23.3 + - - +
100G VAL* 3.4 23.3 - - + -
117G VAL* 5.4 1.6 - - + -
119G HIS* 4.5 24.7 - - + +
154G GLY 4.2 0.2 + - - -
155G VAL* 1.3 78.6 - - - +
157G CYS* 1.3 62.9 - - - +
158G SER* 3.8 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G SER* 3.0 2.6 - - - -
64G PHE* 2.9 68.9 + - + +
87G LEU* 3.9 20.2 - - + -
89G PHE* 4.0 11.7 - - - -
95G PRO* 4.0 10.5 - - - -
96G ILE 3.2 9.6 - - - -
97G VAL* 4.2 9.4 - - + -
155G VAL* 4.4 2.4 + - + -
156G ILE* 1.3 73.0 - - - +
158G SER* 1.3 65.1 + - - +
162G TRP* 3.8 6.1 - - - -
171G ILE* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G GLY 3.1 8.7 - - - -
63G SER* 2.8 23.2 + - - -
95G PRO* 3.5 4.9 - - - +
96G ILE* 2.8 46.5 + - - +
119G HIS* 6.0 0.3 - - - -
156G ILE* 3.8 12.8 - - - +
157G CYS* 1.3 74.2 - - - +
159G SER* 1.3 64.4 + - - +
162G TRP* 3.7 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASP* 3.6 2.3 - - - +
62G GLY 2.9 29.6 + - - +
93G SER* 2.6 29.6 + - - -
94G TYR 4.4 4.0 - - - -
95G PRO* 4.9 0.7 - - - -
96G ILE* 4.5 2.0 - - - +
158G SER* 1.3 78.7 - - - +
160G ALA* 1.3 61.6 + - - +
161G LYS 3.2 14.6 + - - -
162G TRP* 3.2 31.8 + - - -
----------------------------------------------------------
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