Contacts of the strand formed by residues 152 - 162 (chain O) in PDB entry 3HOU
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 152 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O THR* 3.8 25.2 - - + +
54O ASN* 3.4 2.6 - - - -
55O THR* 2.8 33.2 + - - +
56O THR* 4.4 2.3 + - - -
103O ALA 3.3 12.6 - - - +
104O PHE* 4.2 29.4 - - + -
147O LEU* 4.7 1.6 - - - -
150O GLY 3.7 3.5 + - - +
151O GLN* 1.3 76.1 - - - +
153O LEU* 1.3 66.9 + - - +
154O LYS* 3.5 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O THR 3.2 3.6 - - - +
54O ASN* 3.7 27.4 - - + +
56O THR* 3.7 17.7 - - - +
63O ILE* 3.9 22.9 - - + -
101O LEU* 3.3 29.3 - - + +
102O GLN* 3.2 7.0 + - - -
103O ALA* 3.0 38.1 + - + +
113O VAL* 4.5 15.9 - - + -
144O ILE* 5.0 1.6 - - + -
145O CYS* 4.8 6.5 - - - -
147O LEU* 5.0 3.4 - - + -
152O GLU* 1.3 75.9 - - - +
154O LYS* 1.3 59.1 + - - +
155O LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O GLU* 2.9 67.2 + - + +
53O THR* 2.5 16.7 + - - +
100O THR* 5.8 0.4 - - + -
101O LEU 3.4 3.8 - - - +
102O GLN* 3.6 30.5 + - + +
152O GLU* 3.5 24.9 + - + +
153O LEU* 1.3 73.9 - - - +
155O LEU* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O VAL* 4.4 5.6 - - + -
50O GLU 3.6 5.6 - - - +
51O VAL* 3.3 33.9 - - + -
52O GLU* 6.1 0.2 - - - -
54O ASN* 5.3 0.4 - - + -
63O ILE* 4.2 13.2 - - + -
67O LEU* 3.3 31.9 - - + -
100O THR* 3.7 9.0 - - - +
101O LEU* 2.9 56.8 + - + +
153O LEU* 4.0 24.5 - - + -
154O LYS* 1.3 84.4 - - - +
156O THR* 1.3 68.9 + - - +
157O CYS* 4.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O SER 3.6 0.5 - - - +
49O VAL* 3.3 6.1 - - - -
50O GLU* 3.0 57.0 + - - +
52O GLU* 5.8 2.3 - - - +
98O VAL* 3.8 22.9 - - + -
99O LEU 3.6 7.6 - - - +
100O THR* 5.4 4.8 - - + +
155O LEU* 1.3 79.4 + - - +
157O CYS* 1.3 67.1 + - - +
158O VAL* 5.2 3.5 - - + +
64X LEU* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O ILE* 3.5 39.7 - - + -
48O SER 3.4 3.8 - - - -
49O VAL* 4.1 13.7 - - - -
67O LEU* 4.1 13.2 - - - -
98O VAL* 3.0 26.2 - - - +
99O LEU* 2.9 32.1 + - + -
100O THR* 5.7 0.2 - - - -
101O LEU* 5.6 1.3 - - - -
118O LEU* 5.1 5.6 - - - -
155O LEU* 4.7 5.2 - - - -
156O THR* 1.3 83.6 - - - +
158O VAL* 1.3 65.4 + - - +
159O ALA 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O ILE* 4.5 0.8 - - - +
47O ASP* 3.4 18.2 + - - -
48O SER* 3.1 31.4 + - - +
50O GLU* 6.1 1.6 - - + +
91O HIS* 3.3 40.4 - - + +
96O SER* 3.7 21.8 - - - +
97O VAL 3.4 3.8 - - - +
98O VAL* 4.5 6.5 - - + -
156O THR* 5.2 3.8 - - + +
157O CYS* 1.3 84.5 - - - +
159O ALA* 1.3 63.6 + - - +
160O LYS* 3.5 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O LEU* 3.1 38.9 - - + +
45O ALA 3.2 15.0 - - - +
46O ILE* 3.7 7.2 - - - +
72O LEU* 4.2 4.7 - - + -
96O SER* 3.4 8.8 - - - -
97O VAL* 2.8 36.9 + - + +
99O LEU* 4.5 6.8 - - + +
157O CYS 4.0 0.6 - - - -
158O VAL* 1.3 74.9 - - - +
160O LYS* 1.3 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O LEU* 3.4 7.4 - - - -
45O ALA 3.0 17.3 + - - -
47O ASP* 4.4 27.1 + - + +
48O SER* 5.2 4.5 - - - -
83O SER* 3.2 33.4 + - - +
90O ASP* 4.2 19.0 + - - -
91O HIS* 4.7 6.4 + - - -
95O CYS 4.3 7.9 - - - +
96O SER* 4.6 4.9 - - - -
158O VAL* 3.5 27.1 + - + +
159O ALA* 1.3 81.0 - - - +
161O LYS* 1.3 66.3 + - - +
170O TRP* 3.1 21.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O PRO* 3.7 26.6 - - + +
43O THR 3.2 8.1 - - - +
77O ILE* 3.3 38.2 + - + +
78O GLU* 4.1 14.5 + - - +
80O LEU* 3.2 31.6 + - + +
81O GLU* 4.4 9.3 + - - +
82O TYR* 3.6 51.9 - - + +
84O ARG* 5.6 0.5 + - - -
95O CYS 4.7 3.8 + - - -
160O LYS* 1.3 81.0 - - - +
162O GLY* 1.3 61.6 + - - +
170O TRP* 3.7 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O PRO* 3.3 8.3 - - - +
43O THR 2.8 30.7 + - - -
82O TYR* 4.1 8.5 - - - -
161O LYS* 1.3 77.1 - - - +
163O ILE* 1.3 62.1 + - - -
166O GLU* 5.7 2.5 - - - -
170O TRP* 3.3 26.2 - - - +
----------------------------------------------------------
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