Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 3NTY
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 ALA 160 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.3 8.1 - - + -
111A VAL* 3.5 10.5 - - + -
114A TYR* 3.9 21.1 - - + -
154A CYS* 3.3 8.5 + - + +
155A LYS* 3.4 22.7 - - - +
158A GLY* 4.3 3.9 - - - -
159A LEU* 1.3 82.9 - - - +
161A LYS* 1.3 65.1 + - - +
162A SER 3.8 15.7 - - - +
163A ILE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A HIS* 3.4 37.2 + - + +
77A GLU* 6.0 2.2 - - - +
110A TYR* 3.1 55.5 + - + +
111A VAL 3.0 9.6 + - - +
112A ASP* 3.4 21.5 - - + +
155A LYS* 2.8 32.2 + - - +
158A GLY* 5.3 3.8 - - - +
160A ALA* 1.3 74.9 - - - +
162A SER* 1.3 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.6 8.6 - - - +
12A ASP* 2.3 29.2 + - - -
14A HIS* 3.4 15.9 - - - +
80A PHE* 5.0 1.4 - - - -
112A ASP 2.8 14.2 + - - -
113A LEU* 3.3 14.4 - - - -
114A TYR 3.0 20.8 + - - -
155A LYS* 4.4 3.6 - - - +
160A ALA* 3.8 4.0 - - - +
161A LYS* 1.3 72.3 - - - +
163A ILE* 1.3 69.7 + - - +
187A VAL* 3.9 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.9 0.9 - - - -
114A TYR* 3.2 7.6 - - + +
148A TRP* 3.5 26.2 - - + -
151A VAL* 3.5 30.7 - - + +
152A GLU* 3.7 36.3 - - + +
154A CYS* 5.4 0.4 - - + -
155A LYS* 4.2 16.4 - - + +
160A ALA* 4.1 15.7 - - + -
162A SER* 1.3 81.0 - - - +
164A GLY* 1.3 58.8 + - - +
184A TYR* 4.0 17.9 - - + -
185A LYS 4.1 1.3 - - - +
186A PRO* 3.6 1.0 - - - +
187A VAL* 2.9 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR 3.0 7.8 + - - +
115A LEU* 3.2 33.3 - - - +
116A ILE 3.2 5.0 + - - -
148A TRP* 3.6 8.5 - - - -
163A ILE* 1.3 77.0 - - - +
165A VAL* 1.3 65.9 + - - +
186A PRO* 3.9 9.4 - - - -
187A VAL 4.0 2.0 - - - -
188A CYS* 3.7 11.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
115A LEU* 3.7 10.5 - - - +
116A ILE* 3.7 8.1 - - + -
148A TRP* 4.1 13.9 - - + -
164A GLY* 1.3 79.1 - - - +
166A SER* 1.3 63.4 + - - +
168A PHE* 3.6 35.9 - - + -
173A LEU* 3.7 24.2 - - + -
176A ILE* 5.1 2.7 - - + -
186A PRO* 4.0 16.6 - - + -
188A CYS 2.9 21.9 + - - +
189A ASN* 3.4 18.4 - - - +
190A GLN 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 4.8 0.7 - - - -
115A LEU* 4.3 8.3 - - - -
116A ILE 3.0 11.3 + - - +
117A HIS* 3.3 22.6 - - - +
119A PRO* 4.0 1.2 - - - +
165A VAL* 1.3 78.8 - - - +
167A ASN* 1.3 74.0 + - - +
168A PHE* 3.2 13.5 + - - -
189A ASN* 3.6 1.6 - - - -
190A GLN* 2.7 25.5 + - - +
351A NAP 2.8 26.7 + - - -
----------------------------------------------------------
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