Contacts of the strand formed by residues 22 - 29 (chain B) in PDB entry 5CYO
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 PHE 22 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 1.3 74.7 - - - +
23B GLU* 1.3 56.3 + - - +
80B ARG 3.9 18.3 + - - +
81B MET* 3.3 10.3 - - + +
82B LYS 2.4 34.2 + - - +
270B MET* 5.8 8.7 - - + -
274B LYS* 5.3 4.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
21B GLY 3.4 14.7 - - - +
22B PHE* 1.3 74.4 - - - +
24B PHE* 1.3 62.3 + - - +
25B ASN* 4.9 2.9 - - - +
82B LYS* 3.5 15.5 - - + +
128B ILE 4.2 5.5 - - - +
129B PRO* 4.0 9.2 - - - +
130B ASP* 3.2 53.6 + - + +
131B THR* 5.9 0.5 - - - +
134B HIS* 3.8 3.1 - - - -
270B MET* 5.2 0.6 - - - +
274B LYS* 2.7 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE 4.0 0.2 + - - -
23B GLU* 1.3 75.3 - - - +
25B ASN* 1.3 62.1 + - - +
26B ILE* 3.5 34.3 - - + -
81B MET* 4.0 24.0 - - + -
82B LYS 3.0 8.2 + - - +
83B LEU* 3.5 14.3 - - + +
84B THR 2.9 25.3 + - - +
134B HIS* 3.6 24.2 - - + -
135B CYS* 4.6 4.9 - - + -
265B LEU* 3.3 27.4 - - + -
266B ILE* 5.0 2.5 - - + -
270B MET* 3.7 33.7 - - + -
273B ILE* 3.9 21.8 - - + -
274B LYS* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 4.9 2.3 - - - +
24B PHE* 1.3 79.1 + - - +
26B ILE* 1.3 63.7 + - - +
82B LYS 4.9 0.5 - - - +
84B THR* 3.3 30.6 + - - +
86B ILE* 4.6 10.5 - - + -
130B ASP 3.0 27.7 + - - +
131B THR* 3.3 12.0 - - - -
132B ARG 2.7 29.8 + - - +
133B VAL* 4.0 4.1 - - - -
134B HIS* 3.0 39.5 + - - +
135B CYS 3.4 7.1 + - - +
----------------------------------------------------------
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 PHE* 3.5 34.5 - - + -
25B ASN* 1.3 73.9 - - - +
27B MET* 1.3 65.6 + - - +
28B VAL* 5.2 0.4 - - + -
43B LEU* 4.0 25.6 - - + -
83B LEU* 4.0 13.0 - - + -
84B THR 2.7 11.5 + - - +
85B VAL* 3.1 14.8 - - + +
86B ILE* 2.6 37.1 + - - +
135B CYS* 3.4 14.1 - - + +
137B LEU* 4.0 25.6 - - + -
265B LEU* 4.4 16.6 - - + -
266B ILE* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 1.3 76.1 - - - +
28B VAL* 1.3 61.7 + - - +
29B VAL* 3.6 28.0 - - + -
67B ILE* 5.2 0.7 - - + -
86B ILE* 3.5 25.4 - - + +
88B THR* 3.9 9.9 - - + -
104B ILE* 3.8 21.1 - - + -
107B PHE* 3.6 35.0 - - + -
108B ILE* 4.3 14.1 - - + -
133B VAL* 3.7 23.0 - - + +
135B CYS 3.0 7.2 + - - +
136B CYS* 3.3 7.6 - - - -
137B LEU* 2.7 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 5.2 0.7 - - + -
27B MET* 1.3 77.1 - - - +
29B VAL* 1.3 57.1 + - - +
36B LYS* 3.9 16.6 - - + +
39B LEU* 5.8 1.3 - - + -
40B ILE* 3.7 27.4 - - + +
85B VAL* 4.3 8.3 - - + -
86B ILE 3.0 14.5 + - - +
87B ASP* 3.6 23.8 - - - +
88B THR* 2.5 31.1 + - - +
137B LEU* 3.5 16.6 - - + -
139B PHE* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.6 20.0 - - - -
28B VAL* 1.3 80.3 - - - +
30B GLY* 1.3 61.2 + - - +
36B LYS* 3.5 5.2 - - - -
88B THR* 3.7 9.0 - - - +
104B ILE* 4.1 13.2 - - + -
136B CYS* 3.4 28.3 - - - -
137B LEU 2.9 6.5 + - - +
138B TYR* 3.5 20.5 - - + -
139B PHE* 2.8 30.1 + - - +
154B PHE* 3.4 31.2 - - + -
158B LEU* 3.9 4.0 - - + -
----------------------------------------------------------
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