Contacts of the strand formed by residues 668 - 675 (chain S) in PDB entry 1O19
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 668 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S LEU* 6.2 0.6 - - - +
165S PHE* 4.5 22.9 - + - -
169S ASP* 4.7 5.5 + - - -
171S GLU* 4.2 16.3 + - - +
172S ASN 2.7 15.1 + - - +
173S GLN* 2.6 27.7 + - - +
174S SER 3.2 16.5 + - - -
494S HIS* 3.6 20.4 + + - -
498S LEU* 5.3 4.0 - - - +
667S THR* 1.3 69.5 - - - +
669S PRO* 1.3 85.3 + - + +
670S HIS* 3.3 24.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 669 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S LEU* 5.5 2.6 - - - +
174S SER* 3.1 10.8 - - - +
176S LEU* 4.5 1.6 - - + -
490S PHE* 3.5 37.9 - - + -
494S HIS* 3.6 37.6 + - + +
667S THR 3.1 13.4 - - - +
668S HIS* 1.3 106.3 + - + +
670S HIS* 1.3 62.7 + - - +
671S PHE* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 670 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S LEU* 6.2 2.2 - - - +
158S ILE* 4.5 16.8 + - + +
161S ASN* 5.2 3.1 - - + -
162S ALA* 4.1 12.7 - - + -
165S PHE* 3.9 23.4 - + - -
173S GLN* 3.2 34.8 + - + +
174S SER* 2.7 18.4 + - - +
175S ILE* 2.9 17.7 - - + -
176S LEU* 2.7 33.1 + - - +
668S HIS* 3.3 41.6 + + - -
669S PRO* 1.3 72.4 + - - +
671S PHE* 1.3 55.2 + - - +
672S VAL* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 671 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S LEU* 3.7 20.4 + - + +
122S PHE* 3.7 22.4 - + + +
123S CYS* 3.5 18.8 + - - +
158S ILE* 4.4 4.7 - - - +
176S LEU* 3.9 24.7 - - + -
487S LEU 4.8 2.9 - - - -
490S PHE* 4.1 9.0 - + - -
491S PHE* 3.2 55.0 - + + -
494S HIS* 4.2 15.5 - + - -
669S PRO* 3.7 29.4 - - + -
670S HIS* 1.3 71.9 - - - +
672S VAL* 1.3 69.0 + - - +
673S ARG* 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 672 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123S CYS* 3.8 16.4 - - + +
125S THR* 4.9 2.0 - - - +
155S ILE* 4.5 24.7 - - + -
158S ILE* 4.2 20.6 - - + -
175S ILE* 3.8 22.2 - - + -
176S LEU 2.8 21.7 + - - +
177S ILE* 3.3 21.0 - - + -
178S THR 3.3 12.3 + - - -
192S VAL* 6.4 1.1 - - + -
671S PHE* 1.3 79.1 - - - +
673S ARG* 1.3 70.3 + - - +
674S CYS* 4.1 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 673 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122S PHE* 3.9 28.8 - - + -
123S CYS 3.3 10.4 + - - +
124S VAL* 3.4 5.8 - - - -
125S THR* 3.0 24.8 + - - -
176S LEU* 3.0 36.4 + - - +
178S THR* 3.6 29.4 + - - +
484S ASN* 5.4 2.6 + - - -
487S LEU* 5.2 15.6 - - - +
488S GLN* 4.6 9.1 + - - +
491S PHE* 5.9 1.8 - - - +
671S PHE* 3.9 20.8 - - - -
672S VAL* 1.3 76.9 + - - +
674S CYS* 1.3 62.3 + - - +
675S ILE* 3.9 5.8 - - + +
698S ASN* 3.2 51.0 + - + +
700S VAL* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 674 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125S THR* 3.6 8.1 - - - +
177S ILE* 3.5 28.7 - - - -
178S THR 2.9 14.2 + - - +
179S GLY* 3.7 11.1 - - - -
183S ALA* 3.4 31.1 - - + +
185S LYS* 4.2 6.1 - - + -
188S ASN* 2.9 33.2 - - - +
672S VAL* 4.5 7.2 - - - -
673S ARG* 1.3 74.2 - - - +
675S ILE* 1.3 62.8 + - - +
694S GLN* 4.6 2.8 - - - +
698S ASN* 4.8 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 675 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106S LEU* 5.4 2.0 - - + -
124S VAL* 3.0 33.4 - - + -
125S THR 2.5 18.7 + - - +
126S VAL* 3.6 22.4 - - + -
127S ASN* 3.1 29.1 + - - +
183S ALA* 3.9 7.3 - - - +
673S ARG* 3.9 10.3 - - + +
674S CYS* 1.3 76.1 - - - +
676S ILE* 1.3 70.8 + - - +
677S PRO* 4.2 0.7 - - + -
691S VAL* 4.3 17.5 - - + -
694S GLN* 4.1 16.6 - - + +
695S LEU* 4.7 11.9 - - + -
698S ASN* 3.7 23.8 - - - +
700S VAL* 5.7 0.7 - - + -
----------------------------------------------------------
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