Contacts of the strand formed by residues 89 - 94 (chain R) in PDB entry 1HI0
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 HIS 89 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R SER 5.4 0.7 - - - +
51R LEU* 5.1 0.3 - - - +
54R LYS* 3.6 13.3 + - - -
86R GLY 2.7 27.8 - - - -
87R MET 2.7 10.7 + - - +
88R ARG* 1.3 75.8 - - - +
90R MET* 1.3 68.9 + - - +
91R ASN* 3.1 17.4 + - - +
207R SER 3.5 22.9 - - - +
209R ASP* 3.2 38.8 + - + -
210R ALA 5.2 0.2 - - - -
211R ILE* 3.5 21.7 - - + +
247R LYS* 5.0 7.6 - - + -
264R PHE* 4.0 1.2 - - - -
265R PHE* 3.2 13.9 + - + +
266R CYS 3.4 23.6 + - - -
267R GLU* 4.3 12.9 - - + -
268R ARG 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R SER* 4.6 2.0 - - - -
46R VAL* 4.0 18.2 - - + -
51R LEU* 3.2 44.2 - - + -
89R HIS* 1.3 72.0 - - - +
91R ASN* 1.3 64.9 + - - +
93R PHE* 3.0 29.5 + - + +
249R ALA* 4.1 12.1 - - + -
252R LEU* 3.8 29.6 - - + -
258R ILE* 5.2 0.9 - - - -
259R ASP 5.1 1.3 - - - +
260R VAL* 4.6 13.7 - - - -
261R PRO* 5.0 0.4 - - - -
264R PHE* 3.4 29.6 - - + -
265R PHE 2.8 19.0 + - - +
267R GLU* 4.4 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R ALA* 3.7 2.9 - - - -
37R ILE* 3.4 31.4 + - + +
39R THR* 4.6 1.2 + - - -
45R SER* 2.8 38.1 + - - -
54R LYS* 3.1 25.7 - - - +
89R HIS* 3.1 9.5 + - - +
90R MET* 1.3 68.0 - - - +
92R GLY* 1.3 57.4 + - - +
93R PHE* 4.3 0.7 - - - -
207R SER* 3.8 10.4 - - - +
267R GLU* 3.2 22.2 - - - +
526R PHE 3.5 12.3 + - - -
527R SER* 3.6 21.4 + - - +
528R PRO* 4.5 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 92 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R GLU* 3.6 3.3 - - - +
35R GLY 3.0 37.1 + - - +
37R ILE* 3.5 13.5 - - - +
91R ASN* 1.3 73.2 - - - +
93R PHE* 1.3 61.0 + - - +
94R PRO* 3.6 8.2 - - - +
267R GLU* 2.9 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R GLU* 3.4 18.8 - - + +
35R GLY* 3.5 14.6 - - - -
36R ALA* 3.3 34.1 - - - -
46R VAL* 3.8 17.0 - - + -
90R MET* 3.0 19.7 + - + +
91R ASN 4.3 0.4 - - - -
92R GLY* 1.3 78.8 - - - +
94R PRO* 1.3 58.4 - - - +
252R LEU* 3.2 42.8 - - + -
256R TYR* 3.6 18.8 - + - -
258R ILE* 3.7 19.1 - - + -
266R CYS* 3.3 15.0 - - - +
267R GLU* 2.7 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 94 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R PHE* 3.5 26.9 - - + -
34R GLU* 3.4 20.2 - - + +
92R GLY 3.6 8.5 - - - +
93R PHE* 1.3 84.9 - - - +
95R MET* 1.3 68.8 + - - +
96R ILE* 3.8 0.5 + - - +
251R ARG* 3.1 22.2 + - - -
266R CYS* 3.4 5.2 - - - +
267R GLU* 3.4 10.9 - - + +
269R ARG* 3.5 45.5 - - + +
----------------------------------------------------------
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