Contacts of the strand formed by residues 150 - 157 (chain B) in PDB entry 1TNF
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 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.3 24.9 - - - +
18B ALA* 3.3 29.4 + - + -
26B LEU* 4.1 6.3 - - + -
28B TRP* 3.7 15.9 - - + -
61B GLN 3.0 5.4 - - - +
62B VAL* 4.0 13.7 - - + -
63B LEU 4.5 8.1 - - - +
142B LEU* 4.8 6.7 - - + -
143B LEU 3.8 10.8 - - - +
144B PHE* 3.7 30.5 - - + -
146B GLU* 3.7 7.6 - - + +
149B GLN* 1.4 83.9 + - + +
151B TYR* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.4 29.1 - - + +
120A LEU* 4.3 0.9 - - - +
121A GLY 3.5 22.1 + - - -
15B HIS* 3.5 23.8 - + + +
16B VAL 3.1 11.2 - - - +
17B VAL* 5.0 1.3 - - + -
28B TRP* 3.2 15.3 - - - -
59B TYR* 3.5 28.3 - + - -
60B SER* 3.4 6.1 + - - -
61B GLN* 2.7 83.8 + - + +
119B TYR* 3.3 16.6 - + - -
148B GLY* 4.2 9.4 - - - -
149B GLN 4.2 5.6 - - - -
150B VAL* 1.3 76.5 - - - +
152B PHE* 1.3 58.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.4 2.2 + - - -
16B VAL* 2.8 49.1 + - + +
28B TRP* 3.7 33.0 - + + -
46B ASN 5.0 1.8 - - - -
48B LEU* 3.6 31.0 - - + +
58B ILE* 4.1 13.7 - - + -
59B TYR 3.7 11.0 - - - -
60B SER* 4.2 2.7 - - - -
80B ILE* 4.0 20.4 - - + -
132B LEU* 3.6 38.6 - - + -
133B SER* 4.0 1.6 - - - -
134B ALA* 3.8 23.6 - - + -
151B TYR* 1.3 78.9 - - - +
153B GLY* 1.3 61.9 + - - +
154B ILE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 3.0 17.3 - - - -
48B LEU* 5.0 0.9 - - - -
58B ILE* 3.5 0.5 - - - +
59B TYR* 2.9 58.1 + - - +
152B PHE* 1.3 77.1 - - - +
154B ILE* 1.3 67.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO 5.4 0.2 - - - +
13B VAL* 3.3 2.3 - - - -
14B ALA* 2.7 46.9 + - + +
41B VAL* 4.3 19.1 - - + -
48B LEU* 4.1 14.1 - - + -
49B VAL 5.5 0.2 - - - +
50B VAL* 4.0 17.7 - - + -
56B TYR* 4.0 29.8 - - + -
57B LEU 3.3 4.9 - - - +
58B ILE* 3.5 29.4 - - + -
59B TYR* 5.0 0.2 - - - -
132B LEU* 3.6 21.3 - - + -
152B PHE* 5.0 0.4 - - + -
153B GLY* 1.3 81.5 - - - +
155B ILE* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.1 14.6 - - + -
123A VAL* 3.8 28.3 - - + -
157A LEU* 4.8 18.8 - - + -
11B LYS* 4.2 12.3 - - + -
12B PRO 3.6 8.7 - - - +
13B VAL* 3.6 25.8 - - + -
56B TYR* 3.2 6.3 - - - -
57B LEU* 2.8 70.0 + - + +
59B TYR* 4.9 0.7 - - + -
154B ILE* 1.3 75.1 - - - +
156B ALA* 1.3 74.2 + - - +
157B LEU* 3.5 4.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 6.2 0.2 - - - +
11B LYS* 3.1 29.6 - - + +
12B PRO* 3.3 43.4 + - + +
54B GLY* 6.0 2.0 - - - -
55B LEU 3.7 7.2 - - - +
56B TYR* 3.8 12.1 - - + -
155B ILE* 1.3 75.9 - - - +
157B LEU* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.8 19.5 - - + -
11B LYS* 4.9 11.6 + - - +
54B GLY* 5.0 0.2 - - - -
55B LEU* 2.9 29.2 + - - +
57B LEU* 4.1 28.0 - - + +
123B VAL* 4.7 1.1 - - + -
155B ILE* 3.5 6.4 + - + +
156B ALA* 1.3 80.5 - - - +
9C SER* 2.8 38.6 + - - -
11C LYS* 4.0 24.6 - - - -
57C LEU* 5.2 0.2 - - + -
155C ILE* 3.8 47.3 - - + -
156C ALA 5.1 0.4 - - - +
157C LEU* 3.6 26.0 - - + -
----------------------------------------------------------
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