Contacts of the strand formed by residues 114 - 118 (chain B) in PDB entry 1TF4
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 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 4.7 3.4 - - + +
107B ALA* 3.5 21.8 - - + +
108B HIS* 4.3 7.2 - - + -
112B ASN 4.2 0.2 - - - -
113B VAL* 1.3 75.1 - - - +
115B TYR* 1.3 67.3 + - - +
116B VAL* 3.4 21.4 + - + -
142B LYS* 3.3 3.9 - - - -
143B VAL* 2.9 45.1 + - + +
152B VAL* 4.1 2.5 - - + +
153B ALA* 3.8 24.7 - - + +
156B THR* 3.7 32.1 - - + +
185B LEU* 4.0 24.2 - - + -
188B PHE* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.8 32.7 + - + +
47B LEU* 3.4 32.3 - - + +
49B LEU* 3.8 27.1 - - + -
63B GLY* 5.7 0.5 - - - -
103B TYR* 4.7 8.7 + - - +
107B ALA* 2.9 40.9 + - + +
109B PRO* 4.2 6.1 - - + -
113B VAL* 4.1 16.3 - - + +
114B LEU* 1.3 72.7 - - - +
116B VAL* 1.3 61.8 + - - +
117B GLN 3.6 2.5 - - - +
118B VAL* 5.7 0.7 - - + -
140B SER* 4.0 11.2 - - - -
141B PHE 3.3 18.4 - - - +
142B LYS* 3.6 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS 4.3 0.4 - - - -
62B PHE* 4.2 0.2 - - - -
63B GLY* 2.8 32.7 + - - -
64B PHE 4.6 0.3 + - - -
103B TYR* 5.5 1.8 - - - -
114B LEU* 3.4 24.7 + - + +
115B TYR* 1.3 74.8 - - - +
117B GLN* 1.3 61.7 + - - +
141B PHE 3.1 5.3 + - - +
142B LYS* 4.4 1.6 - - - -
143B VAL* 4.0 9.4 - - + -
152B VAL* 3.6 41.1 - - + -
196B TYR* 4.2 10.7 - - + -
200B VAL* 3.5 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.1 8.0 - - + +
61B LYS 3.3 11.9 - - - +
62B PHE* 3.6 19.6 - - + -
103B TYR* 5.2 1.0 + - - -
115B TYR* 3.6 2.3 - - - -
116B VAL* 1.3 85.7 - - + +
118B VAL* 1.3 68.3 + - - +
119B GLY 2.9 24.4 + - - +
120B ASP* 4.4 0.4 - - - +
121B GLY 4.3 7.5 - - - +
139B PRO 3.9 0.2 - - - +
140B SER* 3.5 2.6 - - - -
141B PHE* 2.8 54.1 + - + +
196B TYR* 5.6 0.3 - - - -
200B VAL* 4.2 4.8 - - + +
201B PRO* 4.0 17.6 + - - +
202B ALA* 3.4 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.5 37.9 - - + +
49B LEU* 4.0 29.2 - - + -
60B VAL* 3.7 2.9 - - - +
61B LYS* 3.0 41.8 + - + +
103B TYR* 3.5 20.4 - - - +
115B TYR* 5.7 0.9 - - + -
117B GLN* 1.3 79.0 - - - +
119B GLY* 1.3 64.0 + - - +
138B ARG* 3.9 16.1 + - + +
139B PRO 3.4 6.7 - - - +
140B SER* 4.5 5.4 - - - +
----------------------------------------------------------
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