Contacts of the strand formed by residues 95 - 98 (chain D) in PDB entry 1USK
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 95 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D LYS 3.0 12.2 + - - +
72D TYR* 3.7 12.2 - - + -
73D VAL* 3.0 35.7 + - - +
74D ILE* 5.6 0.4 - - + -
94D ILE* 1.3 79.4 - - - +
96D MET* 1.3 63.7 + - - +
97D ILE* 3.8 35.2 - - + +
113D HIS* 3.6 9.6 - - - +
287D LEU* 4.4 13.9 - - + -
299D PRO* 3.9 25.2 - - + +
302D LEU* 4.1 19.3 - - + -
303D VAL* 3.6 27.6 - - + +
306D LEU* 5.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D VAL* 3.3 9.9 - - + +
75D GLY 3.2 28.5 - - - +
76D HIS* 4.4 0.7 - - - -
82D THR* 3.7 27.8 - - + +
86D SER* 4.2 6.5 - - - -
89D TYR* 3.6 37.0 - - + -
94D ILE 3.6 0.4 + - - +
95D LEU* 1.3 75.5 - - - +
97D ILE* 1.3 60.3 + - - +
98D SER* 3.9 10.8 - - - +
106D LEU* 4.5 2.0 - - + -
113D HIS 3.0 7.7 + - - +
114D ILE* 3.5 40.3 - - + -
115D MET 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D VAL 3.0 6.9 + - - -
74D ILE* 3.5 16.3 - - + +
75D GLY 3.1 17.7 + - - -
95D LEU* 3.8 24.9 - - + -
96D MET* 1.3 75.0 - - - +
98D SER* 1.3 60.8 + - - +
99D PRO* 3.5 2.4 - - - +
115D MET* 3.5 17.7 - - + -
116D ARG* 4.0 23.3 - - - +
117D THR* 4.1 16.6 - - + +
283D ALA* 4.2 22.2 - - + +
286D SER* 4.9 3.8 - - - -
287D LEU* 4.6 11.4 - - + +
306D LEU* 4.2 25.4 - - + -
320D TRP* 5.7 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D GLY 3.2 16.2 + - - -
76D HIS 2.8 18.0 + - - -
82D THR* 3.9 7.1 + - - -
96D MET* 3.9 11.8 - - - +
97D ILE* 1.3 71.1 - - - +
99D PRO* 1.3 63.4 - - - +
100D GLY 3.6 0.3 + - - -
101D ALA* 3.1 27.4 + - - +
106D LEU* 4.5 2.0 - - - -
115D MET 3.2 10.9 + - - -
116D ARG* 3.2 10.8 - - - +
117D THR* 3.1 21.4 + - - -
118D ALA* 3.8 1.6 + - - +
----------------------------------------------------------
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