Contacts of the strand formed by residues 136 - 144 (chain E) in PDB entry 1S9C
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 LEU 136 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E TYR* 3.7 53.9 - - + +
98E LYS* 4.3 7.3 - - - +
129E TYR* 3.8 24.9 - - + -
130E SER 3.5 15.5 - - - +
131E TYR* 3.4 34.2 - - + +
134E LYS 4.3 0.4 + - - -
135E GLU* 1.3 77.0 - - - +
137E ILE* 1.3 60.8 + - - +
138E CYS 3.7 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LEU* 3.6 1.4 - - - -
97E TYR* 2.8 28.0 + - - -
98E LYS* 3.2 25.1 + - + +
99E PRO 4.8 1.6 - - - +
100E LEU* 3.4 32.8 - - + -
101E PRO* 4.4 16.2 - - + -
106E LEU* 3.5 17.5 - - + -
130E SER* 2.8 17.1 + - - +
132E SER* 3.3 28.5 - - - +
135E GLU* 3.7 17.0 - - + +
136E LEU* 1.3 78.5 - - - +
138E CYS* 1.3 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLY* 4.5 14.6 - - - -
64E ILE* 4.5 5.8 - - - -
94E LEU* 4.0 4.3 - - + -
95E GLU 3.2 13.0 - - - +
96E LEU* 3.7 17.7 - - + -
97E TYR* 4.1 4.7 - - - -
100E LEU* 4.5 9.2 - - + -
106E LEU* 5.8 0.2 - - - -
128E VAL 4.1 0.3 - - - +
129E TYR* 3.6 1.9 - - - -
130E SER* 3.0 50.5 + - - -
136E LEU* 3.7 4.2 - - - +
137E ILE* 1.3 84.8 - - + +
139E HIS* 1.3 61.9 + - - +
140E ASN* 4.3 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E TYR* 3.7 24.9 - + - +
94E LEU* 3.3 5.2 - - - +
95E GLU* 2.9 34.2 + - + +
97E TYR* 3.5 30.2 + - + +
127E ASP* 2.6 32.2 + - - -
128E VAL 3.6 7.2 - - - -
129E TYR* 3.7 33.9 + + + +
138E CYS* 1.3 75.9 - - - +
140E ASN* 1.3 89.0 + - - +
141E GLN* 4.5 2.5 - - + -
162E LYS* 4.5 13.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLY 3.0 22.5 + - - -
62E VAL* 3.5 11.3 - - - -
65E GLY* 3.9 12.9 - - - +
92E GLN* 3.2 17.9 + - - +
93E TYR 3.2 2.2 - - - -
94E LEU* 3.4 22.9 - - - +
127E ASP* 3.3 0.9 - - - -
128E VAL* 2.8 41.2 + - + +
130E SER* 4.8 0.8 + - - -
138E CYS* 4.3 8.5 - - - -
139E HIS* 1.3 80.5 - - - +
141E GLN* 1.3 60.9 + - - +
142E PHE* 3.4 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E GLN* 3.9 3.4 + - - -
93E TYR* 2.9 43.6 + - + +
125E ILE* 4.0 14.1 - - + +
126E MET 3.4 5.6 - - - +
127E ASP* 2.8 28.7 + - - +
139E HIS* 4.1 5.1 - - - +
140E ASN* 1.3 71.9 - - - +
142E PHE* 1.3 60.4 + - - +
143E SER* 3.6 7.1 + - - -
160E LYS 3.1 26.3 + - - -
161E VAL* 3.6 11.0 - - - +
162E LYS* 3.0 44.1 + - - +
243E LYS* 4.9 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E VAL* 3.9 14.1 - - + -
65E GLY 3.6 19.7 - - - -
66E GLN* 3.8 23.3 - - + -
68E SER 6.0 1.3 - - - -
89E HIS* 3.9 15.0 - + - +
91E GLU 4.3 0.2 - - - -
92E GLN* 3.1 31.2 - - - -
124E ILE 3.7 2.4 - - - +
125E ILE* 3.7 1.9 - - - -
126E MET* 2.9 49.6 + - + +
128E VAL* 3.4 33.0 - - + -
140E ASN* 3.4 14.4 - - + -
141E GLN* 1.3 73.1 - - - +
143E SER* 1.3 59.8 + - - +
144E LEU* 4.1 16.7 - - + +
217E LEU* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E HIS* 3.6 0.7 - - - -
90E GLY* 2.8 27.7 + - - -
91E GLU* 3.3 46.0 + - - +
123E VAL* 5.8 2.9 - - - +
124E ILE 4.3 1.3 - - - -
125E ILE* 4.4 19.5 - - - +
141E GLN* 3.6 7.0 + - - -
142E PHE* 1.3 70.5 - - - +
144E LEU* 1.3 65.1 + - - +
145E PHE* 4.7 6.2 + - - +
161E VAL* 5.7 1.3 - - - +
243E LYS* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E VAL* 4.0 25.6 - - + -
88E LEU 3.1 9.6 - - - +
89E HIS* 3.8 28.5 - - + -
123E VAL* 3.1 4.4 + - - -
124E ILE* 2.6 64.6 + - + +
126E MET* 5.9 9.6 - - + -
142E PHE* 4.1 18.8 - - + +
143E SER* 1.3 82.3 + - - +
145E PHE* 1.3 59.5 + - - +
146E LEU* 4.5 1.0 - - - +
----------------------------------------------------------
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