Contacts of the strand formed by residues 147 - 155 (chain H) in PDB entry 5LS6
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 147 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G LEU* 4.6 4.7 - - + -
97H PHE* 3.9 8.1 - - - +
116H VAL* 4.0 21.8 - - + -
117H GLY* 4.1 12.0 + - - +
118H SER 3.0 8.3 + - - +
119H ASN* 3.6 20.6 - - - -
120H ARG* 3.6 24.5 - - - -
121H VAL 4.5 2.9 - - - -
140H ASP* 3.8 31.0 - - + -
145H GLU* 3.8 17.5 - - + -
146H ASN* 1.3 84.3 - - - +
148H TYR* 1.3 62.6 + - - +
165H VAL* 3.2 42.8 - - + -
166H ALA* 3.5 15.3 - - - +
167H GLY* 3.7 0.9 - - - -
171H ILE 4.9 2.0 - - - -
173H ARG* 4.1 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H PHE* 3.4 38.4 - + - +
98H GLY 3.8 0.2 + - - -
116H VAL* 3.7 4.7 - - - +
146H ASN* 3.5 30.8 + - - -
147H PHE* 1.3 80.6 - - - +
149H THR* 1.3 57.2 + - - +
166H ALA 2.7 8.2 + - - +
167H GLY* 3.8 0.9 - - - -
168H SER* 3.6 37.8 - - - -
192H ALA* 4.1 9.9 - - + -
193H ILE 3.5 25.6 - - - +
194H ASN* 4.1 10.8 - - - -
365H TYR* 3.2 24.1 + - - +
367H ARG* 4.9 0.5 + - - -
7S M3L 3.9 42.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLY* 5.2 2.0 - - - -
116H VAL* 3.8 7.2 - - - +
147H PHE 3.8 0.4 - - - -
148H TYR* 1.3 80.3 - - - +
150H CYS* 1.3 68.4 + - - +
165H VAL* 3.3 5.2 - - - +
166H ALA 3.0 34.7 + - - +
193H ILE* 3.9 12.8 - - + +
194H ASN 4.0 4.7 - - - -
195H GLU* 3.6 23.0 + - - +
196H LEU* 3.0 45.3 + - + +
365H TYR* 4.5 0.7 - - - -
367H ARG* 5.5 2.5 - - - +
415H GLN* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 150 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H GLY* 5.4 1.2 - - - -
99H VAL 4.7 2.9 - - - -
100H GLN* 3.3 40.5 - - - +
114H ALA* 4.0 25.1 - - - -
116H VAL* 3.5 31.5 - - + +
149H THR* 1.3 82.1 + - - +
151H ALA* 1.3 64.9 + - - +
163H LEU* 3.8 7.6 - - + -
164H ALA 3.0 13.9 - - - +
165H VAL* 3.8 4.7 - - + -
196H LEU* 4.6 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H GLN* 4.3 12.6 - - - +
150H CYS* 1.3 77.7 - - - +
152H TRP* 1.3 64.3 + - - +
163H LEU* 4.0 5.4 - - - -
164H ALA* 3.0 27.4 + - + +
196H LEU* 4.3 26.7 - - + +
197H LYS* 4.6 4.5 - - + -
198H PHE* 3.5 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 152 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H GLN* 2.9 33.0 + - + +
101H PHE 3.2 20.4 - - - +
102H ASN* 3.3 49.5 - - + +
103H TRP 5.1 0.7 - - - +
104H HIS* 3.3 16.9 + - + -
112H VAL* 4.4 6.3 - - + -
113H PHE 4.4 2.5 - - - -
114H ALA* 3.8 23.8 - - + -
123H LEU* 3.7 27.6 - - + -
151H ALA* 1.3 73.8 - - - +
153H THR* 1.3 63.0 - - - +
161H PRO* 4.2 13.9 - - + -
162H LEU 3.4 17.3 - - - -
163H LEU* 3.8 24.4 - - + +
177H PRO* 4.4 10.8 - - + -
198H PHE* 3.9 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H HIS* 3.6 16.0 + - - -
152H TRP* 1.3 76.5 - - - +
154H TYR* 1.3 61.1 + - - +
161H PRO* 3.4 6.2 - - - +
162H LEU* 2.6 60.6 + - + +
174H ILE* 6.0 0.2 - - + -
198H PHE* 3.5 33.9 - - + +
203H PRO* 2.6 39.9 + - - +
220H ILE* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 2.6 54.7 + - + +
65G ILE* 4.1 24.2 - - + -
104H HIS* 3.5 30.7 - + + -
153H THR* 1.3 82.9 + - - +
155H ASP* 1.3 60.5 + - - +
156H SER* 3.3 48.4 + - - -
160H HIS 3.0 16.4 - - - +
161H PRO* 4.2 0.2 - - - -
162H LEU* 3.7 10.5 - - - +
201H ARG 4.9 0.3 + - - -
203H PRO* 3.7 43.7 - - + +
204H ASN* 4.9 3.8 - - - +
220H ILE* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H TYR* 1.3 71.1 - - - +
156H SER* 1.3 55.8 + - - +
157H ASN* 3.0 23.2 + - - +
158H THR* 3.2 31.3 + - - +
159H SER* 2.5 37.1 + - - -
160H HIS* 2.9 13.9 + - + +
162H LEU* 3.6 18.8 - - + +
183H ILE* 5.7 4.0 - - - +
204H ASN* 5.8 2.0 - - - -
----------------------------------------------------------
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