Contacts of the strand formed by residues 123 - 130 (chain B) in PDB entry 2HT6
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 GLU 123 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.5 25.3 - - + +
119B MET* 3.7 5.5 - - - +
120B VAL 3.0 22.8 + - - +
121B ASP 3.2 4.0 - - - +
122B GLY* 1.3 79.7 - - - +
124B SER* 1.3 64.6 + - - +
240B ARG* 2.9 48.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.8 26.0 + - - +
76B TYR* 5.9 0.2 - - - -
117B THR* 3.3 26.3 - - - +
118B LEU 3.4 6.0 + - - -
119B MET* 3.6 12.9 - - - -
123B GLU* 1.3 79.3 - - - +
125B ALA* 1.3 58.4 + - - +
126B THR* 5.1 1.2 + - - -
240B ARG* 3.4 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR 3.7 6.7 - - - +
76B TYR* 4.6 6.3 - - + -
116B ARG 3.7 0.9 - - - +
117B THR* 3.2 3.1 - - - -
118B LEU* 2.7 44.8 + - + +
120B VAL* 4.7 2.2 - - + -
124B SER* 1.3 76.8 + - - +
126B THR* 1.3 62.0 + - - +
127B ILE* 3.7 7.0 + - + -
236B VAL* 3.7 38.4 - - + -
240B ARG* 3.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 4.7 6.1 - - - +
74B THR* 3.0 18.0 + - - -
75B TYR* 3.4 9.8 - - + -
76B TYR 2.9 27.4 + - - +
105B ASP* 3.9 21.3 - - + +
115B GLU* 3.2 28.7 - - + +
116B ARG 3.7 0.2 - - - -
117B THR* 2.9 20.4 + - - +
124B SER* 5.1 1.0 + - - -
125B ALA* 1.3 71.6 - - - +
127B ILE* 1.3 63.0 + - - +
128B ILE* 5.1 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.4 30.3 - - + -
78B VAL* 3.6 31.0 - - + -
95B PHE* 3.6 32.4 - - + -
114B TYR 3.6 0.9 - - - +
115B GLU* 3.2 7.6 - - - +
116B ARG 2.8 35.5 + - - +
118B LEU* 5.1 3.8 - - + -
125B ALA* 4.5 6.5 - - + +
126B THR* 1.3 81.1 - - - +
128B ILE* 1.3 70.2 + - - +
129B LEU* 3.9 4.2 + - + +
232B PHE* 5.7 2.5 - - + +
235B ILE* 5.8 1.1 - - + -
236B VAL* 3.9 31.6 - - + -
239B VAL* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.8 8.7 - - - +
75B TYR* 3.6 24.9 - - + -
76B TYR 3.0 9.5 + - - +
77B ARG* 3.4 29.5 - - + +
78B VAL 2.8 31.9 + - - +
105B ASP* 3.8 15.9 - - - +
107B GLU* 4.0 5.6 - - - +
109B LEU* 4.1 10.8 - - + -
113B THR* 3.4 25.8 - - + -
114B TYR 3.3 2.0 - - - -
115B GLU* 3.6 30.5 - - + -
126B THR* 4.0 1.8 + - + -
127B ILE* 1.3 73.0 - - - +
129B LEU* 1.3 54.8 + - - +
130B LEU* 4.0 4.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.2 33.9 - - + +
80B LEU* 3.7 26.7 - - + -
92B ALA* 3.7 36.8 - - + +
95B PHE* 3.9 29.4 - - + -
112B ASP 3.7 1.0 - - - +
113B THR* 3.3 5.0 - - - -
114B TYR* 2.8 45.6 + - + +
127B ILE* 3.8 4.6 - - + -
128B ILE* 1.3 70.9 - - - +
130B LEU* 1.3 67.5 + - - +
154B LEU* 4.7 0.2 - - + -
232B PHE* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 4.1 20.4 - - + +
78B VAL 2.9 12.4 + - - +
79B VAL* 3.7 20.8 - - + +
80B LEU* 3.0 32.7 + - - +
112B ASP 3.7 2.9 - - - -
113B THR* 3.6 33.9 - - + +
128B ILE* 4.0 9.6 - - + -
129B LEU* 1.3 74.1 - - - +
131B ASP* 1.3 59.9 + - - +
132B MET* 3.7 24.7 - - + -
145B HIS* 4.7 5.4 - - + +
146B CYS* 5.1 4.7 - - - -
149B VAL* 3.5 32.5 - - + -
----------------------------------------------------------
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