Contacts of the strand formed by residues 135 - 139 (chain D) in PDB entry 3NDR
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 135 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ASP 3.1 5.2 + - - +
84D ILE* 3.5 18.7 - - + +
85D LEU 2.9 26.9 + - - +
127D MSE 3.6 3.0 - - - +
133D ALA 4.6 7.2 + - - +
134D GLY* 1.3 78.4 + - - -
136D VAL* 1.3 63.5 + - - +
137D ILE* 4.6 5.2 - - + -
176D ASN 5.3 2.4 + - - -
178D THR* 3.6 35.5 + - - +
226D LEU 3.2 21.5 + - - +
227D ALA* 3.5 16.6 + - - +
228D SER 3.4 23.7 + - - -
229D ASP* 3.0 31.1 + - - +
231D ALA 4.9 2.0 - - - -
232D ARG* 3.8 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LEU* 3.6 9.9 - - + +
87D ASN* 3.9 23.1 - - - +
120D THR* 4.3 12.8 - - + -
124D THR* 3.8 28.5 - - + -
127D MSE 4.3 8.5 - - + -
135D ARG* 1.3 76.1 - - - +
137D ILE* 1.3 70.8 + - - +
138D SER* 4.0 7.2 - - - +
168D LEU* 4.6 6.5 - - + -
177D ILE* 4.1 9.6 - - + -
178D THR* 2.7 21.3 + - - +
179D ALA* 3.4 12.4 - - + -
180D ASN* 2.8 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ILE* 4.6 7.9 - - + -
85D LEU 2.8 14.1 + - - +
86D VAL* 3.2 10.2 - - + +
87D ASN 2.8 23.9 + - - -
135D ARG* 4.6 5.6 - - + -
136D VAL* 1.3 85.1 - - - +
138D SER* 1.3 64.8 + - - +
139D ILE* 4.7 5.6 - - + -
180D ASN* 3.5 8.7 - - + +
182D VAL* 4.1 13.7 - - + -
223D VAL* 3.8 24.9 - - + +
226D LEU* 3.6 46.9 - - + +
227D ALA* 3.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASN* 3.2 30.5 + - - -
116D THR* 5.1 2.5 + - - -
136D VAL* 4.0 6.8 - - - +
137D ILE* 1.3 74.0 - - - +
139D ILE* 1.3 64.3 + - - +
140D ALA 3.3 1.6 + - - -
161D VAL* 3.7 25.1 - - - -
164D PHE* 5.7 4.4 - - - -
165D THR* 4.1 8.2 + - - -
180D ASN 3.0 14.1 + - - -
181D ALA* 3.1 5.7 - - - +
182D VAL 3.0 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ILE* 5.0 1.3 - - + -
23D ILE* 4.2 13.9 - - + -
86D VAL* 3.9 28.7 - - + -
87D ASN 2.9 20.1 + - - +
88D ASN* 4.3 12.6 - - - +
137D ILE* 4.4 7.4 - - + +
138D SER* 1.3 74.1 - - - +
140D ALA* 1.3 62.6 + - - +
158D LYS* 3.1 18.5 + - - +
161D VAL* 4.8 4.1 - - - +
182D VAL* 3.7 10.5 - - + +
184D PRO* 3.9 13.0 - - + -
219D ILE* 4.6 12.3 - - + -
223D VAL* 4.2 10.8 - - + -
251D NAD 3.3 36.9 + - - +
----------------------------------------------------------
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