Contacts of the strand formed by residues 161 - 166 (chain A) in PDB entry 1S9V
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 161 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.8 25.4 - - + -
121A TRP* 4.9 1.6 - - + -
122A LEU 3.2 13.5 - - - +
123A SER* 3.8 20.6 - - - -
124A ASN 4.9 0.2 - - - +
128A VAL* 5.9 0.4 - - + -
151A LEU* 3.8 25.6 - - + -
153A LEU* 3.6 36.4 - - + +
154A LEU 4.0 3.3 + - - -
155A PRO* 5.1 1.7 - - + +
156A SER 5.3 1.1 + - - -
159A GLU* 2.9 45.5 + - + +
160A SER* 1.3 76.8 - - - +
162A ASP* 1.3 65.9 + - - +
177A HIS* 3.0 9.7 + - - -
178A TRP* 2.8 55.4 + + + +
180A PRO* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 3.5 10.9 - - - -
122A LEU* 2.9 44.8 + - + +
125A GLY* 4.9 7.8 + - - -
160A SER* 5.2 2.9 + - - +
161A TYR* 1.3 79.4 - - - +
163A CYS* 1.3 60.2 + - - +
175A LEU* 3.8 28.0 - - + +
176A LYS 3.0 9.4 + - - +
177A HIS* 3.0 38.9 + - - +
178A TRP* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 4.6 0.4 - - + +
91A VAL* 3.5 19.0 - - + +
107A CYS* 2.0 50.7 - - + -
119A ILE* 3.6 20.0 - - - -
120A THR 3.7 4.0 - - - -
121A TRP* 4.2 10.5 - - + -
162A ASP* 1.3 72.6 - - - +
164A LYS* 1.3 60.4 + - - +
165A VAL* 4.2 7.3 - - - +
174A LEU 3.5 1.6 - - - +
175A LEU* 3.3 5.5 - - - -
176A LYS* 2.8 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASN 3.4 1.2 - - - +
119A ILE* 3.3 5.4 - - - +
120A THR* 2.6 60.4 + - - +
122A LEU* 4.5 19.2 - - + +
162A ASP 3.9 0.4 + - - -
163A CYS* 1.3 73.0 - - - +
165A VAL* 1.3 64.2 + - - +
166A GLU* 3.6 24.7 + - - +
173A PRO* 4.0 22.9 - - + +
174A LEU 3.4 2.9 - - - -
175A LEU* 3.6 29.4 - - + -
65E LYS* 3.6 27.5 - - - +
69E GLU* 5.1 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 4.6 4.0 - - + -
89A VAL* 3.7 29.8 - - + -
109A VAL* 3.8 28.0 - - + -
117A VAL* 3.8 23.8 - - + -
118A ASN 3.3 2.2 - - - +
119A ILE* 4.4 3.1 - - + -
163A CYS* 4.2 13.7 - - - +
164A LYS* 1.3 78.1 - - - +
166A GLU* 1.3 63.8 + - - +
170A LEU* 3.7 18.2 - - + +
173A PRO* 3.4 3.9 - - - +
174A LEU* 2.8 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A VAL* 3.4 7.4 - - - +
118A ASN* 2.9 64.3 + - + +
120A THR* 4.8 6.8 + - - +
164A LYS* 3.6 27.0 + - + +
165A VAL* 1.3 77.8 - - - +
167A HIS* 1.3 60.8 + - - +
173A PRO* 4.2 24.7 - - + -
----------------------------------------------------------
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