Contacts of the strand formed by residues 153 - 158 (chain L) in PDB entry 1VYH
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 VAL 153 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L THR* 2.6 31.9 + - - +
126L ALA* 3.8 12.2 - - + +
127L SER 2.8 19.7 + - - +
130L ALA* 3.5 29.4 - - + +
131L THR 3.6 10.1 - - - +
132L ILE* 4.2 11.0 - - + +
149L HIS* 4.3 12.6 - - + -
152L SER* 1.3 75.2 - - - +
154L GLN* 1.3 60.0 + - - +
155L ASP 4.2 5.4 - - - +
167L SER* 4.0 13.9 - - - +
168L CYS 2.9 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J ASP* 5.6 4.4 - - - +
112L THR* 3.6 22.7 - - + +
113L ARG* 2.6 36.3 + - - +
126L ALA* 5.2 0.4 - - - -
128L GLU* 4.2 11.9 + - - -
152L SER* 3.7 22.6 + - - -
153L VAL* 1.3 73.7 - - - +
155L ASP* 1.3 54.6 + - - +
168L CYS 2.7 12.1 + - - -
169L SER 3.8 1.2 - - - -
170L ALA* 3.5 20.9 + - - +
194L ASN* 3.0 29.8 + - - +
195L VAL 3.8 15.3 - - - +
196L SER* 4.1 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ARG* 2.8 39.9 + - - +
126L ALA* 5.1 1.6 - - - -
153L VAL* 4.2 4.3 - - - +
154L GLN* 1.3 75.8 - - - +
156L ILE* 1.3 78.3 + - - +
167L SER* 3.5 4.1 - - - -
168L CYS* 3.2 29.9 + - + +
196L SER 4.1 0.2 - - - +
197L SER* 2.7 34.0 + - - -
198L VAL* 3.0 25.6 + - - +
241L ARG* 3.1 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113L ARG* 4.6 15.7 - - + +
114L VAL 5.0 0.9 - - - -
115L ILE* 3.3 39.5 - - + +
124L VAL* 3.4 24.5 - - + +
126L ALA* 3.7 25.6 - - + +
132L ILE* 3.6 22.2 - - + -
155L ASP* 1.3 90.8 + - - +
157L SER* 1.3 63.3 + - - +
165L LEU* 3.7 18.8 - - + -
166L ALA 3.3 8.3 - - - +
167L SER* 4.6 5.6 - - - -
198L VAL* 4.4 1.4 - - - +
241L ARG* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L ILE* 3.6 5.6 - - - -
156L ILE* 1.3 76.5 - - - +
158L PHE* 1.3 68.5 + - - +
165L LEU* 3.7 6.4 - - - +
166L ALA* 2.9 33.4 + - - -
198L VAL* 3.7 8.1 - - - -
199L SER* 3.4 23.8 - - - -
200L ILE* 2.8 29.6 + - - +
241L ARG* 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L ILE* 3.5 37.9 - - + +
116L PHE 3.9 10.5 - - - +
117L HIS* 3.4 37.0 - + - -
118L PRO* 4.2 11.0 - - + -
124L VAL* 3.7 11.9 - - + -
157L SER* 1.3 82.6 + - - +
159L ASP* 1.3 68.4 + - - +
162L GLY* 4.0 9.4 - - - -
164L LEU 3.5 13.5 - - - -
165L LEU* 4.1 10.1 - - + -
179L PHE* 3.4 47.6 - + + -
200L ILE* 3.9 6.6 - - - +
----------------------------------------------------------
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