Contacts of the strand formed by residues 155 - 162 (chain E) in PDB entry 1S9V
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 PHE 155 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASP* 5.0 3.4 - - + -
29D ASP* 4.3 5.8 - - - -
121E ASP* 3.2 10.2 + - - -
122E PHE* 2.7 45.9 + - + +
123E TYR* 3.6 22.9 - + - -
124E PRO 4.0 0.7 - - - -
125E ALA* 3.5 40.2 - - + -
147E LEU* 3.8 28.5 - - + -
148E ILE 3.2 16.6 - - - +
149E ARG* 3.8 51.6 - - + -
150E ASN* 3.7 3.5 + - - +
154E THR* 1.3 77.0 - - - +
156E GLN* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D PHE* 3.8 10.4 - - - -
93D SER 3.1 27.4 + - - +
94D LYS* 3.5 15.6 + - - +
95D SER 5.9 0.3 - - - -
119E VAL 3.4 12.6 - - - +
120E THR* 4.0 14.1 - - + +
122E PHE* 3.7 4.0 - - - -
147E LEU* 4.0 0.9 - - - +
148E ILE* 2.7 65.7 + - + +
150E ASN* 2.8 25.5 + - - +
155E PHE* 1.3 76.6 - - - +
157E ILE* 1.3 63.5 + - - +
158E LEU* 3.6 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E CYS 3.7 1.4 - - - +
119E VAL* 3.0 43.2 + - + +
122E PHE* 4.1 14.1 - - + -
127E ILE* 4.6 11.2 - - + -
129E VAL* 4.3 16.4 - - + -
144E SER* 3.5 20.2 - - - +
145E THR* 3.6 22.7 - - - +
146E PRO* 4.0 2.5 - - + +
147E LEU* 4.3 15.5 - - + +
148E ILE* 4.9 0.7 - - - -
156E GLN* 1.3 78.1 - - - +
158E LEU* 1.3 68.7 + - - +
159E VAL* 4.0 8.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E VAL* 4.2 19.1 - - + -
117E CYS 3.6 2.9 - - - +
118E SER* 3.9 26.2 - - - +
119E VAL 4.9 0.7 - - - +
120E THR* 5.0 2.0 - - + -
143E VAL 4.0 0.5 - - - +
144E SER* 3.4 1.7 - - - -
145E THR* 2.9 50.3 + - + +
148E ILE* 5.1 4.7 - - + -
156E GLN* 3.6 23.3 - - - +
157E ILE* 1.3 82.4 - - - +
159E VAL* 1.3 63.5 + - - +
160E MET* 3.9 8.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E CYS* 2.9 34.4 + - + +
119E VAL* 5.3 0.2 - - + -
129E VAL* 3.6 46.0 - - + +
130E ARG* 6.0 0.2 - - - -
131E TRP* 3.2 31.6 + - + +
142E VAL* 3.8 18.4 - - + -
143E VAL 3.6 3.4 - - - +
144E SER* 3.9 18.6 - - - +
157E ILE* 4.4 11.2 - - + +
158E LEU* 1.3 73.2 - - - +
160E MET* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E LEU* 4.1 24.0 - - + -
115E LEU 3.3 5.6 - - - +
116E VAL* 3.8 28.7 - - + -
131E TRP* 4.1 0.9 - - - -
141E GLY 4.4 0.2 - - - -
142E VAL* 3.2 8.8 - - - +
143E VAL* 2.6 68.3 + - + +
145E THR* 3.9 28.7 - - + +
158E LEU* 4.1 8.3 - - + +
159E VAL* 1.3 76.1 - - - +
161E LEU* 1.3 61.5 + - - +
162E GLU 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E LEU* 3.4 5.0 - - - +
115E LEU* 2.7 40.9 + - + +
131E TRP* 3.7 48.5 - - + +
132E PHE 5.4 0.4 - - - +
138E GLU* 4.2 17.5 - - + -
140E ALA 4.4 3.8 - - - +
141E GLY 3.5 5.4 - - - +
142E VAL* 3.7 22.2 - - + -
160E MET* 1.3 75.7 - - - +
162E GLU* 1.3 76.3 + - - +
163E MET* 3.7 10.6 + - + +
171E TYR* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ASN 3.0 34.1 + - - +
114E LEU* 3.6 14.2 - - + +
140E ALA 5.1 0.7 - - - +
141E GLY* 2.8 28.6 + - - +
143E VAL* 6.4 0.7 - - + -
161E LEU* 1.3 78.8 - - - +
163E MET* 1.3 72.1 + - - +
----------------------------------------------------------
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