Contacts of the strand formed by residues 19 - 26 (chain B) in PDB entry 5T4S
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 GLN 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B THR 3.3 2.6 - - - +
14B ASN* 3.7 1.7 - - - +
15B TYR* 2.8 59.7 + - + +
18B THR* 1.3 90.3 + - - +
20B TYR* 1.3 62.3 + - - +
21B TYR* 3.9 14.3 - - + -
121B LEU* 3.0 24.1 + - - +
123B GLU* 2.8 31.0 + - - +
124B PHE* 3.3 23.1 - - + -
402B 77O 3.8 23.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.5 6.4 - - + +
13B THR 3.3 4.7 - - - -
14B ASN* 3.1 30.1 + - + -
17B ASP* 3.3 17.6 + - - -
19B GLN* 1.3 76.0 - - - +
21B TYR* 1.3 63.4 + - - +
36B VAL* 3.7 10.9 - - - +
37B PHE 4.5 1.9 + - - -
162B TYR* 3.5 57.0 + + + -
163B ASN 2.7 21.7 + - - -
173B GLY 3.3 28.3 - - - -
174B GLY* 5.0 1.3 - - - -
317B ALA* 3.7 23.6 - - + -
321B ARG* 3.1 18.2 + - - -
402B 77O 3.2 23.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PRO* 4.6 8.3 + - - +
12B LEU* 3.9 7.3 - - - +
13B THR* 2.8 65.2 + - + +
15B TYR* 3.7 27.6 - - + +
19B GLN* 3.9 16.6 - - + -
20B TYR* 1.3 77.7 - - - +
22B GLY* 1.3 57.4 + - - +
34B LYS* 3.8 38.4 + - + +
35B VAL 3.1 24.9 - - - +
36B VAL* 4.1 0.9 - - + +
37B PHE* 5.2 0.4 - - - -
123B GLU* 3.5 29.6 + - + +
124B PHE* 3.8 18.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.0 0.7 - - - -
11B ILE 3.6 17.9 - - - -
12B LEU* 3.7 12.6 - - - +
21B TYR* 1.3 75.2 - - - +
23B GLU* 1.3 64.3 + - - -
34B LYS* 3.3 4.8 - - - -
35B VAL* 2.6 41.3 + - - +
37B PHE* 3.9 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 3.6 26.4 + - + +
283A ASP* 3.7 12.0 - - - +
322A LYS* 2.5 38.8 + - - -
10B VAL* 3.8 22.0 - - + +
11B ILE 4.6 4.8 + - - +
22B GLY* 1.3 78.5 - - - +
24B ILE* 1.3 66.9 + - - +
32B THR* 3.7 22.2 - - + +
33B PHE 3.3 6.7 - - - +
34B LYS* 5.0 4.7 - - + -
37B PHE* 5.0 0.2 - - - -
98B THR 4.3 2.6 - - - +
99B VAL* 4.9 1.6 - - - -
100B GLY 4.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLY 4.2 0.2 + - - -
23B GLU* 1.3 79.9 - - - +
25B GLY* 1.3 57.9 + - - +
26B ILE* 4.0 26.2 - - + -
31B GLN 3.6 0.7 - - - +
32B THR* 3.4 5.1 - - - -
33B PHE* 2.9 32.7 + - + +
35B VAL* 3.8 34.1 - - + -
37B PHE* 3.9 13.0 - - + -
44B VAL* 4.5 7.4 - - + -
46B VAL* 4.7 1.1 - - + -
97B ILE* 4.0 15.3 - - + -
98B THR 3.2 13.5 - - - +
99B VAL* 3.9 19.7 - - + -
128B VAL* 3.8 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 1.3 73.1 - - - +
26B ILE* 1.3 61.2 + - - -
27B GLY 4.3 0.4 - - - -
30B PRO* 4.2 16.6 - - - -
31B GLN 3.3 10.1 - - - -
32B THR* 4.5 4.0 - - - -
96B ILE 4.3 0.7 - - - -
97B ILE* 3.1 11.1 - - - +
98B THR* 2.8 40.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.0 13.2 - - + -
25B GLY* 1.3 79.0 - - - +
27B GLY* 1.3 62.9 + - - +
29B PRO 3.9 1.4 - - - +
31B GLN* 2.9 36.8 + - - +
33B PHE* 3.7 16.4 - - + -
44B VAL* 5.3 0.7 - - + -
46B VAL* 3.7 40.4 - - + -
64B PHE* 3.5 27.8 - - + -
95B ASP* 3.8 8.1 - - + -
96B ILE 3.5 1.6 - - - -
97B ILE* 3.8 20.0 - - + -
108B PHE* 3.7 28.0 - - + -
----------------------------------------------------------
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