Contacts of the strand formed by residues 149 - 158 (chain B) in PDB entry 5TIN
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 VAL 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 5.0 1.6 - - - +
147B MET 5.6 0.9 - - - +
148B ASP* 1.3 77.5 - - - +
150B GLN* 1.3 75.1 + - - +
151B THR* 5.4 1.3 + - - +
190B LYS* 6.0 1.3 - - + -
215B HIS* 4.8 11.2 - - + +
216B LEU 3.3 24.2 - - - +
217B GLU* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 4.9 0.9 - - - -
139B PRO 4.4 1.6 - - - +
140B MET* 3.2 32.4 - - + -
141B ASP* 2.8 45.9 + - - +
142B LEU* 4.0 6.1 - - - +
148B ASP* 2.8 33.2 + - - +
149B VAL* 1.3 79.3 + - - +
151B THR* 1.3 64.0 + - - +
152B CYS* 4.1 12.8 - - - -
187B PHE* 4.9 7.0 - - + -
214B PHE 3.7 0.3 - - - +
215B HIS* 3.6 3.6 - - - -
216B LEU* 2.9 43.6 + - + +
218B ARG* 4.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 3.5 9.0 - - - -
139B PRO* 4.6 6.6 + - - +
149B VAL* 5.6 0.9 - - - +
150B GLN* 1.3 75.4 + - - +
152B CYS* 1.3 63.0 + - - +
153B ILE* 4.1 6.4 + - + +
213B ARG* 3.8 44.9 - - + +
214B PHE 3.3 10.1 - - - +
215B HIS* 3.3 25.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 5.2 0.2 - - + -
51B ILE* 5.6 0.7 - - - -
58B TYR* 3.6 28.9 - - + -
138B CYS* 2.1 45.8 - - - -
140B MET* 5.0 4.9 - - - -
150B GLN* 4.1 5.1 - - - -
151B THR* 1.3 73.8 - - - +
153B ILE* 1.3 61.3 + - - +
213B ARG* 3.6 0.7 - - - -
214B PHE* 2.8 41.2 + - + +
216B LEU* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 2.7 25.5 + - - -
102B ASN* 2.9 33.1 + - + +
136B LEU* 4.4 0.2 - - - +
137B SER 4.9 4.1 + - - +
138B CYS* 5.0 1.2 - - - +
139B PRO* 6.3 1.8 - - + -
151B THR* 4.5 6.5 - - + +
152B CYS* 1.3 78.2 - - - +
154B MET* 1.3 57.7 + - - +
155B GLN* 3.8 33.2 - - + +
211B GLU* 4.1 11.2 - - + +
212B VAL 3.3 8.5 - - - +
213B ARG* 3.9 36.3 - - + +
214B PHE* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.9 28.7 - - + -
45B ILE* 5.4 0.4 - - + -
58B TYR* 4.0 3.1 - - - +
60B VAL* 4.0 20.4 - - + -
62B ILE* 4.5 10.5 - - + -
100B PHE* 3.9 27.6 - - + -
102B ASN* 3.8 3.6 - - - +
134B LEU* 4.7 0.4 - - - -
136B LEU* 3.8 24.2 - - + -
153B ILE* 1.3 75.3 - - - +
155B GLN* 1.3 62.4 + - - +
156B LEU* 3.8 18.4 - - + +
211B GLU* 3.3 4.2 - - - -
212B VAL* 3.0 38.0 + - + -
214B PHE* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 3.2 10.9 - - - +
101B ALA* 3.1 37.2 + - + +
102B ASN* 3.1 17.5 + - - +
153B ILE* 3.8 24.8 - - + +
154B MET* 1.3 75.8 - - - +
156B LEU* 1.3 60.6 + - - +
157B GLU 4.0 0.2 - - - -
198B CYS* 3.5 17.6 - - - +
200B LYS* 3.2 26.8 + - - +
209B CYS* 4.0 6.7 - - - -
210B ILE 3.4 3.6 - - - -
211B GLU* 3.0 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B CYS* 4.3 12.6 - - + -
43B ILE* 4.8 1.6 - - + -
64B LEU* 4.0 18.8 - - + -
98B LEU* 4.0 26.2 - - + -
99B PHE 3.7 4.0 - - - -
100B PHE* 3.8 24.7 - - + -
154B MET* 3.8 22.4 - - + +
155B GLN* 1.3 76.0 - - - +
157B GLU* 1.3 59.4 + - - +
168B PHE* 3.6 9.1 - - + -
170B TRP* 4.0 29.6 - - + -
209B CYS* 3.2 2.9 - - - -
210B ILE* 2.7 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.3 4.0 - - - -
99B PHE* 2.8 62.6 + - + +
101B ALA* 3.3 10.2 - - + +
156B LEU* 1.3 74.2 - - - +
158B SER* 1.3 72.2 + - - +
168B PHE* 3.5 7.1 - - - -
200B LYS* 2.8 39.4 + - + +
202B TYR* 2.7 33.8 + - - -
207B PHE* 4.6 2.9 - - + +
208B THR 3.4 14.8 - - - +
209B CYS* 3.8 7.6 - - + -
63C PHE* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP* 2.8 22.4 + - - -
99B PHE* 3.7 1.3 - - - -
157B GLU* 1.3 85.5 - - - +
159B PHE* 1.3 60.2 - - - +
161B TYR* 3.1 36.5 + - - +
166B LEU* 3.9 10.5 - - - -
168B PHE* 3.6 4.7 - - - -
207B PHE* 3.4 15.0 - - - +
208B THR* 3.2 27.2 + - - -
----------------------------------------------------------
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