Contacts of the strand formed by residues 238 - 242 (chain A) in PDB entry 6VSB
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 238 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.0 76.3 + - + +
85A PRO 4.1 2.9 - - - -
86A PHE* 4.6 2.2 - + + -
90A VAL* 3.5 45.5 - - + -
92A PHE* 4.8 6.7 - + - -
104A TRP* 4.2 16.6 - + - -
105A ILE 3.4 6.7 - - - -
106A PHE* 3.5 46.7 - + + -
194A PHE* 5.6 0.9 - + - -
237A ARG* 1.3 80.9 - - - +
239A GLN* 1.3 66.3 + - - +
240A THR* 4.7 5.4 - - - -
265A TYR* 5.9 0.2 - + - -
267A VAL* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.5 32.2 + - + +
82A PRO 4.2 10.1 - - - +
83A VAL* 4.3 16.9 - - + +
84A LEU* 5.5 0.7 - - - -
104A TRP* 4.6 0.2 - - - -
105A ILE* 2.9 36.8 + - + +
110A LEU* 4.2 17.0 - - + +
136A CYS 4.7 3.6 - - - +
137A ASN 4.9 4.4 + - - -
138A ASP* 5.2 2.0 + - - +
139A PRO* 3.5 38.6 + - - +
238A PHE* 1.3 79.0 - - - +
240A THR* 1.3 75.0 + - - +
241A LEU* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 4.0 11.8 - - + +
82A PRO 5.2 0.4 + - - -
84A LEU* 5.8 1.2 - - - +
92A PHE* 4.3 7.5 - - - -
101A ILE* 3.9 11.2 - - + +
103A GLY 3.1 14.6 + - - -
104A TRP* 3.7 20.3 + - - -
139A PRO* 5.1 0.5 - - - +
238A PHE* 4.6 4.9 - - - -
239A GLN* 1.3 94.9 + - - +
241A LEU* 1.3 83.3 + - - +
242A LEU* 4.4 2.6 + - + -
265A TYR* 3.5 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE* 3.7 8.3 - - - +
102A ARG* 3.5 25.5 + - + -
103A GLY* 2.8 38.5 + - - +
104A TRP* 3.7 8.5 - - - +
105A ILE* 3.6 28.5 - - + -
120A VAL* 3.8 28.9 - - + -
139A PRO* 4.5 18.6 - - + +
140A PHE* 5.4 2.9 - - - +
141A LEU* 5.5 8.1 - - + -
159A VAL* 4.7 10.5 - - + -
240A THR* 1.3 96.0 + - - +
242A LEU* 1.3 60.8 + - - +
243A ALA 4.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS 5.6 3.1 - - - +
79A PHE* 4.0 34.8 - - + +
80A ASP 6.1 0.2 - - - -
81A ASN* 5.2 16.8 - - + -
100A ILE* 4.2 19.1 - - + -
101A ILE* 5.9 4.5 - - + -
138A ASP* 5.5 0.5 - - - +
139A PRO 4.1 6.7 + - - +
140A PHE* 3.1 19.6 - - - +
141A LEU* 5.8 0.2 - - - -
240A THR* 4.3 2.2 + - + -
241A LEU* 1.3 73.7 - - - +
243A ALA* 1.3 78.5 + - - +
244A LEU* 4.3 1.7 - - - -
262A ALA* 4.5 18.2 - - + -
263A ALA 5.0 8.1 - - - +
265A TYR* 5.5 9.4 - - + -
----------------------------------------------------------
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