Contacts of the strand formed by residues 96 - 101 (chain H) in PDB entry 1DU3
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 SER 96 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ARG* 3.1 15.8 - - - +
93H GLU* 3.0 26.0 + - - +
95H ASP* 1.3 83.5 - - - +
97H PRO* 1.3 64.1 - - - +
98H GLU 3.2 3.8 + - - -
99H MET 3.4 6.2 - - - +
101H ARG* 2.9 42.1 - - - +
203J ASP 6.0 0.2 - - - -
205J GLN* 3.5 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ARG* 3.0 32.8 + - + +
93H GLU 3.3 8.7 - - - +
94H GLU 3.8 7.9 - - - +
95H ASP 3.6 4.5 - - - -
96H SER* 1.3 89.2 - - - +
98H GLU* 1.3 59.6 + - + +
99H MET 3.5 0.4 - - - -
147J LEU* 3.9 32.7 - - + +
148J GLY 5.3 0.7 - - - +
207J VAL* 5.4 0.9 - - + -
209J TYR* 3.3 23.3 - - + +
261J THR* 4.0 13.7 - - + -
134K ASN* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ARG* 4.7 0.4 - - - -
96H SER 3.2 1.8 - - - -
97H PRO* 1.3 79.5 - - - +
99H MET* 1.3 61.9 + - - +
147J LEU* 5.7 1.6 - - - +
205J GLN* 3.3 9.2 + - - +
207J VAL* 3.8 24.5 - - + -
209J TYR* 3.7 19.5 + - - +
224J LYS* 2.9 41.3 + - - +
226J ALA* 4.7 0.7 - - + -
189K TYR* 2.6 33.0 + - - +
191K ARG* 3.4 24.6 + - - -
239K LEU* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H PHE 4.0 0.3 - - - +
92H ARG* 3.8 9.3 - - - +
96H SER 3.4 15.4 - - - +
97H PRO 3.5 1.0 - - - -
98H GLU* 1.3 78.1 - - - +
100H CYS* 1.3 73.2 + - - +
101H ARG* 3.3 8.1 + - - +
205J GLN* 3.0 22.2 + - - +
191K ARG* 3.0 54.5 - - + +
192K PHE 4.1 9.6 - - - +
193K GLN* 3.2 29.6 - - - +
237K TYR* 3.6 35.9 - - + -
239K LEU* 3.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 100 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H GLY* 3.6 16.2 - - - +
70H GLU* 4.7 2.2 - - - -
86H CYS* 2.0 52.5 - - - -
90H THR* 3.1 17.6 - - - +
91H PHE 3.4 4.9 - - - -
92H ARG* 3.4 14.1 - - - -
99H MET* 1.3 75.2 - - - +
101H ARG* 1.3 64.7 + - - +
102H LYS 3.6 0.2 + - - -
193K GLN* 2.8 36.1 + - - +
237K TYR* 5.1 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H THR* 3.1 2.1 - - - -
91H PHE* 3.0 55.1 + - + +
93H GLU* 3.3 30.5 + - - +
96H SER* 2.9 29.9 + - - +
99H MET 3.7 3.4 - - - +
100H CYS* 1.3 71.4 - - - +
102H LYS* 1.3 66.7 + - - +
201J LYS* 3.2 36.0 + - - +
203J ASP* 2.9 46.1 + - - +
205J GLN* 3.3 21.8 - - - +
237K TYR* 4.1 7.6 - - - +
----------------------------------------------------------
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