Contacts of the strand formed by residues 157 - 163 (chain B) in PDB entry 4DVH
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 ARG 157 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B CYS* 4.0 1.3 - - - -
132B VAL* 2.9 43.2 + - + +
134B PRO* 3.9 32.5 - - + +
138B ASN* 5.8 0.2 - - - -
152B LEU* 5.7 0.4 - - - -
155B GLY 4.5 1.8 + - - +
156B LEU* 1.3 75.4 - - - +
158B PRO* 1.4 67.9 - - - +
159B VAL* 3.6 2.6 + - - +
199B GLN 4.5 4.0 + - - -
200B ALA* 3.0 50.5 + - + +
201B ILE* 5.4 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.0 29.2 - - + -
81B PHE* 3.4 20.7 - - + -
129B TRP* 3.6 31.2 - - + -
131B CYS* 3.8 12.3 - - - -
151B PRO* 4.4 8.1 - - + -
152B LEU* 4.0 13.2 - - + -
156B LEU 3.4 11.9 - - - +
157B ARG* 1.4 86.0 - - - +
159B VAL* 1.3 60.8 + - - +
196B MET* 4.0 11.3 - - + +
200B ALA* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.5 14.5 - - - -
85B CYS* 4.3 0.5 - - - -
97B LEU* 4.9 1.3 - - + -
130B LEU* 2.9 34.2 + - + +
131B CYS* 4.5 0.9 - - - -
132B VAL* 4.1 13.0 - - + -
140B LEU* 4.6 4.5 - - + -
157B ARG 4.0 7.2 - - - +
158B PRO* 1.3 78.7 - - - +
160B LEU* 1.4 60.6 - - - +
192B PHE* 4.7 0.3 - - - -
193B VAL* 3.4 48.6 - - + +
196B MET* 3.7 7.8 - - - +
197B HIS* 3.4 40.6 - - + +
200B ALA* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.7 5.3 - - - -
85B CYS* 3.8 23.6 - - + -
111B PHE* 4.3 6.5 - - + -
115B PHE* 4.1 23.1 - - + -
129B TRP* 3.1 10.4 - - - +
130B LEU* 2.9 38.7 + - + +
159B VAL* 1.4 76.8 - - - +
161B ALA* 1.4 69.0 + - - +
162B VAL* 4.3 2.7 - - + -
185B TRP* 4.0 15.7 - - + -
188B ILE* 3.9 25.8 - - + -
190B TRP* 3.9 28.7 - - + -
193B VAL* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN 4.5 0.2 - - - +
81B PHE* 3.8 12.1 - - + -
82B TYR* 3.4 32.0 - - - +
85B CYS* 3.8 7.7 - - - +
127B TRP* 4.4 7.9 - - + -
128B THR 3.6 4.5 - - - -
129B TRP* 3.4 37.2 - - + -
160B LEU* 1.4 76.5 - - - +
162B VAL* 1.3 67.5 + - - +
188B ILE* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.8 2.5 - - - -
115B PHE* 3.5 30.3 - - + -
127B TRP* 3.4 5.1 - - - -
128B THR* 2.8 32.9 + - - +
160B LEU* 4.3 12.3 - - + -
161B ALA* 1.3 79.6 - - - +
163B ASP* 1.3 65.5 + - - +
164B VAL* 4.2 2.2 - - + +
180B TYR* 3.8 15.9 - - + +
181B LEU* 3.8 28.9 - - + -
184B ILE* 4.2 24.2 - - + -
185B TRP* 5.7 0.7 - - + -
188B ILE* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 2.9 7.8 + - - -
79B HIS* 3.2 3.5 + - - -
82B TYR* 3.5 20.5 - - + -
126B GLY 3.5 0.7 - - - +
127B TRP* 3.5 26.7 - - + -
162B VAL* 1.3 71.2 - - - +
164B VAL* 1.3 59.8 + - - +
165B TRP* 3.1 36.4 + - - +
168B ALA* 3.7 18.8 - - + +
180B TYR* 2.6 32.9 + - - -
301B FE 1.9 32.7 - - - -
----------------------------------------------------------
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