Contacts of the strand formed by residues 92 - 98 (chain D) in PDB entry 4K9N
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 LEU 92 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 3.9 24.7 - - + -
54D ALA 3.9 23.3 - - - +
55D ASP* 3.9 13.5 - - + -
58D ALA* 3.9 10.8 - - + -
65D ALA* 3.6 9.6 - - + -
67D ILE* 4.0 14.1 - - + -
82D LEU* 4.4 5.2 - - + -
85D ALA* 3.6 27.6 - - + -
90D SER* 3.0 16.6 + - - +
91D PRO* 1.3 80.3 - - - +
93D ILE* 1.3 62.2 + - - +
94D VAL* 4.4 2.9 - - + -
146D ALA* 4.4 0.7 - - - -
152D GLY 3.7 2.7 + - - +
153D PRO* 3.3 8.8 - - + +
154D VAL* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 3.8 28.3 - - + -
64D PRO* 3.9 20.9 - - + -
65D ALA 2.9 13.2 + - - +
66D PHE* 4.0 23.2 - - + -
67D ILE* 2.8 31.2 + - - +
92D LEU* 1.3 73.9 - - - +
94D VAL* 1.3 59.3 + - - +
95D THR* 4.3 8.5 - - + -
139D MET* 4.4 4.9 - - - -
142D ALA* 4.1 26.9 - - + +
143D ILE* 3.9 18.4 - - + +
146D ALA* 4.0 16.2 - - + -
154D VAL* 3.9 4.0 - - + -
156D LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 5.3 1.6 - - + -
67D ILE* 4.0 24.2 - - + -
69D LEU* 3.9 28.3 - - + -
75D THR* 5.6 0.7 - - + -
82D LEU* 4.1 31.4 - - + -
92D LEU* 4.3 7.6 - - + +
93D ILE* 1.3 74.6 - - - +
95D THR* 1.3 66.5 + - - +
123D VAL* 5.8 0.4 - - + -
153D PRO* 5.0 1.3 - - + -
154D VAL 2.9 21.0 + - - +
155D TYR* 3.2 25.3 - - + -
156D LEU* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 5.0 0.7 - - - -
66D PHE* 3.6 35.4 - - + -
67D ILE 2.8 21.8 + - - +
68D ASN* 3.0 19.1 + - - -
69D LEU* 2.8 27.3 + - - +
93D ILE* 4.3 5.8 - - + -
94D VAL* 1.3 79.6 - - - +
96D ALA* 1.3 63.0 + - - +
139D MET* 4.0 19.5 - - + -
155D TYR* 5.0 0.2 - - - -
156D LEU* 3.2 15.7 - - + -
158D VAL* 5.6 4.5 - - - -
163D TRP* 6.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASN* 4.6 2.7 - - - +
69D LEU* 3.1 13.9 - - + +
71D SER* 4.1 9.4 - - - +
75D THR* 3.5 13.0 - - - +
95D THR* 1.3 76.9 - - - +
97D GLY* 1.3 62.7 + - - +
112D ASN* 4.9 1.3 - - - +
155D TYR* 3.4 30.3 - - + +
156D LEU 2.9 7.0 + - - +
157D SER* 3.4 5.5 - - - -
158D VAL* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASN* 3.3 16.9 + - - -
28D GLU* 2.9 30.5 + - - +
68D ASN* 4.7 0.6 - - - +
69D LEU 3.2 1.8 + - - -
71D SER* 3.1 28.1 + - - -
96D ALA* 1.3 73.8 - - - +
98D GLN* 1.3 60.7 + - - -
112D ASN* 5.0 1.4 + - - +
157D SER* 5.1 0.8 + - - -
158D VAL* 3.6 7.6 - - - -
163D TRP* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ASN* 3.3 15.3 - - - +
71D SER* 4.9 0.4 - - - -
97D GLY* 1.3 73.4 - - - -
99D GLN* 1.3 89.6 + - - +
104D ILE* 3.7 23.5 - - + +
110D LEU 4.8 0.2 - - - -
111D THR* 3.5 8.2 - - - +
112D ASN* 2.8 52.1 + - + +
115D ALA* 4.2 0.2 - - - +
128D GLU* 3.0 26.4 + - - +
157D SER* 3.5 15.3 - - - +
158D VAL 2.9 6.0 + - - +
159D PRO* 3.6 17.5 - - + -
160D TYR* 2.9 17.5 + - - -
----------------------------------------------------------
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