Contacts of the strand formed by residues 38 - 43 (chain B) in PDB entry 4XCS
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 TYR 38 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 1.3 77.0 - - - +
39B VAL* 1.3 60.2 + - - +
70B ASN* 3.1 7.2 + - - +
71B CYS* 3.2 18.1 - - + -
72B GLN 2.8 24.3 + - - -
132B ILE* 3.9 20.9 - - + -
133B ILE 3.3 15.0 - - - -
134B ASP* 3.3 26.5 - - + +
135B ASP* 3.6 19.0 - - + +
140B ARG* 3.8 5.1 + - + -
160B VAL* 4.2 10.8 - - + -
163B PHE* 3.3 34.1 - + + +
164B GLN* 3.6 37.0 - - + +
167B ASP* 2.6 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.2 26.0 - - + +
34B TYR* 3.9 26.5 - - + +
37B LYS 3.9 8.7 - - - +
38B TYR* 1.3 80.9 - - - +
40B VAL* 1.3 74.8 + - - +
41B PHE* 4.0 4.7 - - + +
71B CYS* 4.3 0.7 - - - -
72B GLN* 3.1 13.0 - - + +
74B ILE* 4.2 13.5 - - + -
131B PHE 3.4 4.7 - - - +
132B ILE* 3.6 3.6 - - - +
133B ILE* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 1.3 71.9 - - - +
41B PHE* 1.3 59.8 + - - +
42B PHE* 4.6 5.8 - - + -
59B PHE* 4.5 13.5 - - + -
66B PHE* 4.0 11.0 - - + -
71B CYS* 3.6 22.0 - - - -
72B GLN 2.9 5.9 + - - +
73B VAL* 3.3 15.3 - - + +
74B ILE 2.9 27.5 + - - +
130B LEU* 3.9 23.8 - - + -
131B PHE 3.5 3.8 - - - -
132B ILE* 4.1 8.1 - - + -
156B THR* 4.1 10.8 - - + -
160B VAL* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.7 30.7 - + - -
31B LEU* 5.3 2.5 - - + -
39B VAL* 3.7 5.3 - - + -
40B VAL* 1.3 73.7 - - - +
42B PHE* 1.3 58.2 + - - +
43B PHE* 3.7 34.3 - + - -
74B ILE* 3.3 30.5 - - + -
76B ALA* 3.6 22.4 - - + -
105B VAL* 4.6 2.7 - - + -
112B ILE* 4.4 2.9 - - + -
116B TYR* 3.8 36.8 - + - -
130B LEU* 3.8 0.4 - - - -
131B PHE* 2.8 51.6 + + + +
133B ILE* 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.6 8.1 - - + -
41B PHE* 1.3 75.7 - - - +
43B PHE* 1.3 60.6 + - - +
44B TYR* 3.9 23.1 - + - -
55B GLU* 4.3 25.6 - - - -
56B ILE* 4.1 20.6 - - + -
59B PHE* 4.4 15.3 - + + -
73B VAL* 3.8 24.7 - - + -
74B ILE 3.0 16.4 + - - -
75B GLY* 3.4 18.7 - - - -
76B ALA* 2.8 32.8 + - - +
102B ILE* 4.2 13.0 - - + -
129B GLY 3.2 11.0 - - - +
130B LEU* 4.4 11.9 - - + -
151B ARG* 4.1 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.7 35.0 + + - -
42B PHE* 1.3 72.9 - - - +
44B TYR* 1.3 59.8 + - - +
76B ALA* 3.2 20.9 - - + -
77B SER* 4.0 22.0 - - - -
78B VAL 4.5 0.2 - - - -
105B VAL* 6.0 0.2 - - + -
107B ASP* 4.1 7.0 - - + -
112B ILE* 3.7 16.4 - - + -
113B ALA* 3.7 37.7 - - + -
116B TYR* 4.3 5.4 - - + -
118B VAL* 4.0 13.5 - - + -
126B SER* 3.5 24.5 - - - +
127B PHE 4.2 1.3 - - - +
128B ARG* 3.4 4.7 - - - -
129B GLY* 2.9 39.7 + - - +
131B PHE* 4.3 8.7 - + - -
151B ARG* 3.5 7.3 + - - -
----------------------------------------------------------
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